GROMACS version:2020.1-1
GROMACS modification: No
Here post your question
Dear experts.
I’m trying to grompp POPG membrane (Slipid) protein simulation. But I confront an error message which I could not solve with my own knowledge. Also, it seems that there is not much information about using Slipid on gromacs.
So please allow me to ask you a question.
Please forgive me for writing short sentences to convey information as clear as possible.
0. I tried to generate a .tpr file for a POPG-only system using grompp.
**1. I downloaded **
POPG.itp
POPG.pdb
Slipids_2020.ff.tar.gz
md.mdp (example of mdp file which distributed from Stockholm lipids)
sample.top (Sample topology file which distributed from Stockholm lipids)
**2. ‘Slipids_2020.ff.tar.gz’ was unpacked in directory. **
‘sample.top’ was modified according to
↓↓↓↓ start ↓↓↓↓
#include “./Slipids_2020.ff/forcefield.itp”
#include “POPG.itp”
[ system ]
; Name
POPG128
[ molecules ]
; Compound #mols
POPG 1 (actually, I also cannot understand how could I increase lipid molecule number from 1 (in slipid-distributed files) to 128 (to make bilayer membrane). but it is not a main problem here)
↑↑↑↑ end ↑↑↑↑
3. commend ‘gmx grompp -f md.mdp -c POPG.pdb -p sample.top -o popg.tpr’ was entered
4. script was received
↓↓↓↓ start ↓↓↓↓
Command line:
gmx grompp -f md.mdp -c POPG.pdb -p sample.top -o popg.tpr
Ignoring obsolete mdp entry ‘ns_type’
WARNING 1 [file md.mdp]:
The Berendsen barostat does not generate any strictly correct ensemble,
and should not be used for new production simulations (in our opinion).
For isotropic scaling we would recommend the C-rescale barostat that also
ensures fast relaxation without oscillations, and for anisotropic scaling
you likely want to use the Parrinello-Rahman barostat.
Setting the LD random seed to 1609293671
WARNING 2 [file ffnonbonded.itp, line 78]:
Atomtype Na was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 3 [file ffnonbonded.itp, line 83]:
Atomtype HAL1 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 4 [file ffnonbonded.itp, line 84]:
Atomtype HL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 5 [file ffnonbonded.itp, line 85]:
Atomtype HEL1 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 6 [file ffnonbonded.itp, line 86]:
Atomtype CL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 7 [file ffnonbonded.itp, line 87]:
Atomtype CTL1 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 8 [file ffnonbonded.itp, line 88]:
Atomtype CTL3 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 9 [file ffnonbonded.itp, line 89]:
Atomtype CTL2 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 10 [file ffnonbonded.itp, line 90]:
Atomtype HAL3 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 11 [file ffnonbonded.itp, line 91]:
Atomtype HAL2 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 12 [file ffnonbonded.itp, line 92]:
Atomtype CTL5 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 13 [file ffnonbonded.itp, line 93]:
Atomtype CEL1 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 14 [file ffnonbonded.itp, line 94]:
Atomtype CET1 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 15 [file ffnonbonded.itp, line 95]:
Atomtype OBL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 16 [file ffnonbonded.itp, line 96]:
Atomtype OCL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 17 [file ffnonbonded.itp, line 97]:
Atomtype O2L was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 18 [file ffnonbonded.itp, line 98]:
Atomtype OSL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 19 [file ffnonbonded.itp, line 99]:
Atomtype OSLP was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 20 [file ffnonbonded.itp, line 100]:
Atomtype NTL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 21 [file ffnonbonded.itp, line 101]:
Atomtype PL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 22 [file ffnonbonded.itp, line 102]:
Atomtype HOL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 23 [file ffnonbonded.itp, line 103]:
Atomtype OHL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 24 [file ffnonbonded.itp, line 104]:
Atomtype NH3L was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 25 [file ffnonbonded.itp, line 105]:
Atomtype HCL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 26 [file ffnonbonded.itp, line 106]:
Atomtype Na was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 27 [file ffnonbonded.itp, line 107]:
Atomtype CCL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 28 [file ffnonbonded.itp, line 108]:
Atomtype HBL was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 29 [file ffnonbonded.itp, line 109]:
Atomtype NH1 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 30 [file ffnonbonded.itp, line 110]:
Atomtype H11 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 31 [file ffnonbonded.itp, line 134]:
Atomtype OW was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 32 [file ffnonbonded.itp, line 135]:
Atomtype HW was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
Generated 4465 of the 4465 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 4378 of the 4465 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘POPG’
turning all bonds into constraints…
NOTE 1 [file sample.top, line 10]:
System has non-zero total charge: -1.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.
WARNING 33 [file sample.top, line 10]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net
Charge
J. Chem. Theory Comput. 10 (2014) pp. 381-393
-------- -------- — Thank You — -------- --------
NOTE 2 [file unknown]:
You are using constraints on all bonds, whereas the forcefield has been
parametrized only with constraints involving hydrogen atoms. We suggest
using constraints = h-bonds instead, this will also improve performance.
atom name 58 in sample.top and POPG.pdb does not match (C210 - 0C21)
atom name 58 in sample.top and POPG.pdb does not match (C210 - 0C21)
atom name 59 in sample.top and POPG.pdb does not match (H101 - 1H10)
atom name 59 in sample.top and POPG.pdb does not match (H101 - 1H10)
atom name 60 in sample.top and POPG.pdb does not match (C211 - 1C21)
atom name 60 in sample.top and POPG.pdb does not match (C211 - 1C21)
atom name 63 in sample.top and POPG.pdb does not match (C212 - 2C21)
atom name 63 in sample.top and POPG.pdb does not match (C212 - 2C21)
atom name 66 in sample.top and POPG.pdb does not match (C213 - 3C21)
atom name 66 in sample.top and POPG.pdb does not match (C213 - 3C21)
atom name 69 in sample.top and POPG.pdb does not match (C214 - 4C21)
atom name 69 in sample.top and POPG.pdb does not match (C214 - 4C21)
atom name 72 in sample.top and POPG.pdb does not match (C215 - 5C21)
atom name 72 in sample.top and POPG.pdb does not match (C215 - 5C21)
atom name 75 in sample.top and POPG.pdb does not match (C216 - 6C21)
atom name 75 in sample.top and POPG.pdb does not match (C216 - 6C21)
atom name 78 in sample.top and POPG.pdb does not match (C217 - 7C21)
atom name 78 in sample.top and POPG.pdb does not match (C217 - 7C21)
atom name 81 in sample.top and POPG.pdb does not match (C218 - 8C21)
atom name 81 in sample.top and POPG.pdb does not match (C218 - 8C21)
atom name 106 in sample.top and POPG.pdb does not match (C310 - 0C31)
atom name 106 in sample.top and POPG.pdb does not match (C310 - 0C31)
atom name 109 in sample.top and POPG.pdb does not match (C311 - 1C31)
atom name 109 in sample.top and POPG.pdb does not match (C311 - 1C31)
atom name 112 in sample.top and POPG.pdb does not match (C312 - 2C31)
atom name 112 in sample.top and POPG.pdb does not match (C312 - 2C31)
atom name 115 in sample.top and POPG.pdb does not match (C313 - 3C31)
atom name 115 in sample.top and POPG.pdb does not match (C313 - 3C31)
atom name 118 in sample.top and POPG.pdb does not match (C314 - 4C31)
atom name 118 in sample.top and POPG.pdb does not match (C314 - 4C31)
atom name 121 in sample.top and POPG.pdb does not match (C315 - 5C31)
atom name 121 in sample.top and POPG.pdb does not match (C315 - 5C31)
atom name 124 in sample.top and POPG.pdb does not match (C316 - 6C31)
atom name 124 in sample.top and POPG.pdb does not match (C316 - 6C31)
WARNING 34 [file unknown]:
17 non-matching atom names
atom names from sample.top will be used
atom names from POPG.pdb will be ignored
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Program: gmx grompp, version 2022.3
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 3077)
Fatal error:
Group POPC referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the ‘-n’ option
of grompp.
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
(base) root@DESKTOP-D6QVEHV:/kshdownload/PTG3#
↑↑↑↑ end ↑↑↑↑
I guess that I would barely understand other warning messages.
**But I cannot understand the fatal error message. **
Should I generate ‘index file’ with ‘gmx make_ndx’?
(I hope not. In my understanding, ‘Slipid’ are hard to be ‘SPECIAL index groups’)
or do I just need to fix the sample.top file?
Or if anyone knows any information about how to use ‘Slipid’, it would be very thanks if I could acquire a link.
**I referred [gmx-users] How to combine Slipid FF with amber FF? **
but those answers seem to be not applicable to this problem.