Mismatch of topology and solv.gro

topol.top (1.3 KB)
GROMACS version: 2020.2
GROMACS modification: Yes/No
I am trying to setup a simulation of protein ligand system. the topology for the ligand was prepared using the ATB server. I downloaded the forcefield file from the server as the ligand itp file had some different atom types not found in the usual gromacs file. I have attached my top file

When I reach the “add ions” stage , grompp throws the error of

Fatal error:
number of coordinates in coordinate file (solv.gro, 23481)
does not match topology (topol.top, 23482)


I have calculated the number of SOL molecules, they are correct in both the solv.gro and the topology file. the number of atoms at top of the solv.gro is also correct. I checked the number of atoms in complex.gro and box.gro. they are the same. i tried changing the box types also but no difference. 1 atom difference remains.
This is not my first time preparing the files but first time for this system. i have checked the forum for similar issues, and see that it is a common issue but resolutions vary.
Could you help me understand the problem of 1 atom difference.

topol.top (1.3 KB)


Box.gro

GROup of MAchos and Cynical Suckers
903
23SER N 1 1.485 2.372 2.501
23SER H1 2 1.432 2.332 2.576
23SER H2 3 1.576 2.398 2.534
23SER H3 4 1.438 2.453 2.466
23SER CA 5 1.499 2.273 2.394
23SER CB 6 1.360 2.226 2.347
23SER OG 7 1.370 2.139 2.235
.
.
.
.
101RIM CG3 901 2.234 2.907 2.970
101RIM H1 902 2.733 2.994 2.914
101RIM H2 903 2.827 3.074 3.038
6.23112 6.23112 6.23112

RIM is my ligand. Does it hav anything to do with my hydrogen atoms that I added to match the itp file?
because without the hydrogens , another error comes for “no molecule defined in the system”.

solv.gro
GROup of MAchos and Cynical Suckers
23481
23SER N 1 1.485 2.372 2.501
23SER H1 2 1.432 2.332 2.576
23SER H2 3 1.576 2.398 2.534
23SER H3 4 1.438 2.453 2.466
.
.
.
7627SOL OW23479 6.014 6.010 6.106
7627SOL HW123480 6.044 5.938 6.044
7627SOL HW223481 5.975 5.970 6.189
6.23112 6.23112 6.23112

I have calculated the number of molecules and is correct in the topology file

grep -o ‘SOL’ solv.gro | wc -l
22578

22578/3 = 7526

Hello Ayesha! Have you solve the problem? I face the problem too

I am also having an issue with my solv.gro and topology.top matching. All of my mismatches coorespond to my ligands coodinates. I ran the max warn 2 to complete my tpr.

I ran the tuitorial lysozyme ligand 3htb tutorial with similar .gro and .top files so it ignoring my solv.gro ligand atom names should not be a problem? I do my ligands need to be included for adding ions and how?

Do not use -maxwarn to override warnings. Solve the underlying issues. If you need help with how to do that, you need to provide more information about what the warnings stated.

Justin,

Great to hear from you! Your tuitorials are excellent.

I have followed the 3HTB complex tuitorial to my enzyme and two ligands.
I have completed the ligand topologies and added to my protein topology along with creating a complex.gro with all 3 molecules.
created a dodecahedron
solvated my complex in my dodecahedron
and when I grompp to create my Ions.tpr it doesnt recognize my ligands as if they should be in the topology file beyond the .prm and .itp

atom name 7271 in topol.top and solv.gro does not match (P - C1)
atom name 7271 in topol.top and solv.gro does not match (P - C1)

atom name 7272 in topol.top and solv.gro does not match (O1 - C2)

atom name 7272 in topol.top and solv.gro does not match (O1 - C2)

atom name 7273 in topol.top and solv.gro does not match (O2 - C3)

atom name 7273 in topol.top and solv.gro does not match (O2 - C3)

atom name 7274 in topol.top and solv.gro does not match (O3 - C4)

atom name 7274 in topol.top and solv.gro does not match (O3 - C4)

atom name 7275 in topol.top and solv.gro does not match (O4 - C5)

atom name 7275 in topol.top and solv.gro does not match (O4 - C5)

atom name 7276 in topol.top and solv.gro does not match (O5 - C6)

96 lines cooresponding to the lines of my solv.gro that a labeled with my ligands.

WARNING 1 [file topol.top, line 68721]:
  96 non-matching atom names
  atom names from topol.top will be used
  atom names from solv.gro will be ignored


Analysing residue names:
There are:   472    Protein residues
There are:     2      Other residues
There are: 15754      Water residues

thank you for your input.

Derek

You are using coordinates that have atoms in a different order from the topology. They need to be consistent. If you use the files generated by the CGenFF conversion script, they will match. Do not try to bypass this problem; your simulation will instantly fail.

I succesfully ran cgenff_charmm2gmx_py3_nx2.py on both ligands.

python cgenff_charmm2gmx_py3_nx2.py GDPV GDPV_fix.mol2 GDPV.str charmm36-jul2021.ff
NOTE 1: Code tested with Python 3.5.2 and 3.7.3. Your version: 3.7.3 | packaged by conda-forge | (default, Dec  6 2019, 08:54:18) 
[GCC 7.3.0]

NOTE 2: Code tested with NetworkX 2.3. Your version: 2.3

NOTE 3: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation:
--Version of CGenFF detected in  GDPV.str : 4.5
--Version of CGenFF detected in  charmm36-jul2021.ff/forcefield.doc : 4.6

WARNING: CGenFF versions are not equivalent!


NOTE 4: To avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF.
============ DONE ============
Conversion complete.
The molecule topology has been written to gdpv.itp
Additional parameters needed by the molecule are written to gdpv.prm, which needs to be included in the system .top

PLEASE NOTE: If your topology has lone pairs, you must use GROMACS version 2020 or newer to use 2fd construction
Older GROMACS versions WILL NOT WORK as they do not support 2fd virtual site construction

============ DONE ============

Is there another way to get this file in order?
do I need to paste the .prm to my bondedff?

The coordinate file produced by the conversion script should have the atoms in the same order as the corresponding topology. Just as in the tutorial, convert those the *ini.pdb file to .gro format to build the complex. If you have a mismatch, it means you used a different coordinate file for this purpose.

Thank you! this helped me see the root of the issue. My order was off. I went back a few steps and reprocessed my .mol2 and .str files with charm2gmx and completed a clean grompp.