[gmx-users] md with multiple ligands

Ansuman Biswas ansuman at physics.iisc.ernet.in
Mon Feb 18 16:21:21 CET 2013

---------------------------- Original Message ----------------------------
Subject: md with multiple ligands
From:    ansuman at localhost
Date:    Mon, February 18, 2013 8:28 pm
To:      gmx-users at gromacs.org

Message: 8
>> Date: Wed, 13 Feb 2013 08:28:00 -0500
>> From: Justin Lemkul <[hidden email]>
>> Subject: Re: [gmx-users] md with multiple ligands
>> To: Discussion list for GROMACS users <[hidden email]>
>> Message-ID: <[hidden email]>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> On 2/13/13 5:24 AM, Ansuman Biswas wrote:
>>> Dear gromacs users,
>>> I wish to run a protein ligand md in Gromacs 4.5.3 with charmm force
>>> field. Its a dimeric protein with a MG ion and 2 ligands bound to two
>>> active sites. I wish to run the dimer and there would be 4 ligands. I
>>> generated the topology files (.itp) of ligands using SWISSPARAM. Before
>>> running the energy minimization I changed the topol.top file accordingly
>>> as mentioned in the SWISSPARAM website. I added all the itp files
>>> together.But while running GROMPP I got an error message like,
>>> WARNING 1 [file ADP.itp, line 24]:
>>>     Overriding atomtype NPYL
>>> WARNING 2 [file ADP.itp, line 25]:
>>>     Overriding atomtype C5A
>>> WARNING 3 [file ADP.itp, line 26]:
>>>     Overriding atomtype N5B
>>> WARNING 4 [file ADP.itp, line 27]:
>>>     Overriding atomtype C5B
>>> Generated 25425 of the 25425 non-bonded parameter combinations
>>> Generating 1-4 interactions: fudge = 1
>>> Generated 22285 of the 25425 1-4 parameter combinations
>>> -------------------------------------------------------
>>> Program grompp, VERSION 4.5.3
>>> Source code file: toppush.c, line: 1071
>>> Fatal error:
>>> Atoms in the .top are not numbered consecutively from 1 (rather, atomnr
>>> =
>>> 1, while at->nr = 40)
>>> I know that the problem is related to the merging of 4 itp files.
>>> Please let me how I should do that.
>> The ligands probably use common atom types and each .itp file likely has
>> an
>> [atomtypes] directive that introduces these new types.  Probably the
>> easiest
>> thing to do is create a merged [atomtypes] directive that lists all of the
>> necessary atom types so you don't list them separately in each file.  One
>> approach that I have used in the past is to create an .itp file that only
>> has
>> atom types in it, then call something like:
>> #include "charmm27.ff/forcefield.itp"
>> ; only has [atomtypes]
>> #include "my_ligand_atomtypes.itp"
>> ; these don't introduce [atomtypes] any more
>> #include "ligand1.itp"
>> #include "ligand2.itp"
>> -Justin
> But according to SWISSPARAM website I can only add one ligand.itp file.
«  [hide part of quote]

Just a guess, but it's probably because each ligand.itp file introduces
new atom
types which give the conflicts above.

> So, is it possible to add ligand1 and ligand2 itp files?

Sure, my method should work.  Please try it.  I have done the exact same
with Amber topologies from acpype.

> Will it be ok if I merge all the ligand pdbs and then get the combined itp
> file using that from SWISSPARAM and follow the protocol for one ligand?

Merging the coordinate files will probably not work.  If you have multiple
molecules, you need multiple topologies.


Well, I have tried using the method you mentioned; i.e using 2 separate
itp files and use one common atomtype at the beginning. But it seemed that
gromacs was unable to read the next lig1 and lig2 itp files without
atomtypes option. It gave error message. So I tried merging two itp files
from swissparam so that only unique parameters remain in the combined.itp
file. I could run Energy Minimization only with steepest descent but not
with CG as CG could not reduce the maximum force beyond 5th order. After
that when I tried running NVT, I found Lincs error and saw several bonds
rotated beyond 30 deg, as well as domain decomposition error:
        constraint lengths are too long compared to the domain
decomposition cell size

*******More on that when I opened the em.pdb (em output) in pymol I found
all the ligand atoms were jumbled up together.

please help,


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