Error in use of GROMPP

User discussions
1

GROMACS version: 2020.1-1
GROMACS modification: NO
Here post your question
Hii, I am carrying out ligand-receptor MD study. With command,
“gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1”
I am facing major errors with .prm and .itp files. I am not able to resolve this problem. Please guide me to sort out this error.

Your help is much appreciated.

Thanks;
Ashish

"The errors are:

WARNING 1 [file unk.prm, line 4]:
Bondtype Bond 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.

old: 0.137 309616 0.137 309616
new: CG2R64 NG311 1 0.13550000 326352.00

WARNING 2 [file unk.prm, line 11]:
Bondtype U-B 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.

old: 121.7 552.288 0 0 121.7 552.288 0 0
new: NG2R62 CG2R64 NG311 5 120.000000 652.704000 0.00000000 0.00

WARNING 3 [file unk.prm, line 19]:
Bondtype U-B 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.

old: 114 384.928 0 0 114 384.928 0 0
new: CG2R64 NG311 CG321 5 113.000000 460.240000 0.00000000 0.00

WARNING 4 [file unk.prm, line 20]:
Bondtype U-B 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.

old: 113.5 364.008 0 0 113.5 364.008 0 0
new: CG2R64 NG311 HGPAM1 5 115.000000 376.560000 0.00000000 0.00

ERROR 1 [file unk.prm, line 34]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 2 [file unk.prm, line 35]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 3 [file unk.prm, line 51]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 4 [file unk.prm, line 57]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 5 [file unk.prm, line 60]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations

ERROR 6 [file unk.itp, line 135]:
No default Bond types

ERROR 7 [file unk.itp, line 136]:
No default Bond types

ERROR 8 [file unk.itp, line 451]:
No default U-B types

ERROR 9 [file unk.itp, line 455]:
No default U-B types

ERROR 10 [file unk.itp, line 457]:
No default U-B types

ERROR 11 [file unk.itp, line 458]:
No default U-B types

ERROR 12 [file unk.itp, line 477]:
No default U-B types

ERROR 13 [file unk.itp, line 478]:
No default U-B types

ERROR 14 [file unk.itp, line 479]:
No default U-B types

ERROR 15 [file unk.itp, line 651]:
No default Proper Dih. types

ERROR 16 [file unk.itp, line 652]:
No default Proper Dih. types

ERROR 17 [file unk.itp, line 653]:
No default Proper Dih. types

ERROR 18 [file unk.itp, line 654]:
No default Proper Dih. types

ERROR 19 [file unk.itp, line 655]:
No default Proper Dih. types

ERROR 20 [file unk.itp, line 656]:
No default Proper Dih. types

ERROR 21 [file unk.itp, line 666]:
No default Proper Dih. types

ERROR 22 [file unk.itp, line 667]:
No default Proper Dih. types

ERROR 23 [file unk.itp, line 668]:
No default Proper Dih. types

ERROR 24 [file unk.itp, line 687]:
No default Proper Dih. types

ERROR 25 [file unk.itp, line 690]:
No default Proper Dih. types

ERROR 26 [file unk.itp, line 693]:
No default Proper Dih. types

2

Don’t use -maxwarn as it will allow you to bypass potentially significant problems.

The remainder of the warnings indicate your ligand topology has parameters that already exist in the force field (likely coming from a version mismatch between the CGenFF web server and the provided CHARMM36 port that I can do nothing about, sorry).

The missing parameters warnings indicate that parameters that should be in the ligand topology are not there. Check to make sure you haven’t edited those out inappropriately.

3

Ohk… I will check it again

Thanks !

4

Hi,

Thanks for the valuable information. Now I could manage to resolve 21 out of 26 errors, but not able to solve 5 errors.

Could you please guide me to resolve these?

With Regards,
Ashish

The errors are,

ERROR 1 [file unk.prm, line 34]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 2 [file unk.prm, line 35]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 3 [file unk.prm, line 51]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 4 [file unk.prm, line 57]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 5 [file unk.prm, line 60]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

5

This is the same problem as before. Your ligand topology defines dihedrals that already exist in ffbonded.itp. Remove them from the ligand .prm file.

6

Thanks! It worked

7

Dear ashish

How did you solve these errors?
ERROR 26 [file unk.itp, line 693]:
No default Proper Dih. types

8

@ainne your problem is different. Please start a new topic with a more complete description of what you are doing and how you generated your topology.

9

Hope you are resolved with your problem.

10

@ashish
How did you solve your problem, I have the same problem but not getting how to solve it. Any suggestions will really help me to solve this problem.
Thanks
Sadaf

11

Hello Sadaf, sorry for late replying…

If u still have same problem, you can resolve it simply by deleting the lines from your file as Justin has suggested " This is the same problem as before. Your ligand topology defines dihedrals that already exist in ffbonded.itp. Remove them from the ligand .prm file."

13

I am facing same type of problem. How to solve it

ERROR 1 [file unk.itp, line 600]:
No default Proper Dih. types

ERROR 2 [file unk.itp, line 614]:
No default Proper Dih. types

ERROR 3 [file unk.itp, line 634]:
No default Proper Dih. types

ERROR 4 [file unk.itp, line 644]:
No default Proper Dih. types

ERROR 5 [file unk.itp, line 652]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘UNK’
Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 72404]:
System has non-zero total charge: -3.000000
Total charge should normally be an integer. See
GROMACS - Gromacs
for discussion on how close it should be to an integer.

There were 2 notes

Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928)

Fatal error:
There were 5 errors in input file(s)

14

Dear Ashish, How did you solve 6-26 errors(unk.itp)?
Thanks

15

Hi, I would be grateful if you make fix it from the errors below, Thank you in advance.

WARNING 1 [file h71.prm, line 69]:
Bondtype U-B 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.

old: 110 365.682 0 0 110 365.682 0 0
new: CG321 CG321 NG311 5 112.200000 365.681600 0.00000000 0.00

ERROR 1 [file h71.prm, line 163]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 2 [file h71.prm, line 167]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 3 [file h71.prm, line 182]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

16

Pls, fix this also.

gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr

Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 117519 of the 167910 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’

Excluding 3 bonded neighbours molecule type ‘JZ4’

Excluding 2 bonded neighbours molecule type ‘SOL’

ERROR 1 [file topol.top, line 24633]:
No such moleculetype CL