[gmx-users] Query regarding the addition of solvent molecule
jalemkul at vt.edu
Fri Sep 5 13:55:56 CEST 2014
On 9/5/14, 7:10 AM, Christina Florina wrote:
> I have included the chx.itp file in the protein.top file already.
> Checked with the molecule name (CHX) in the .itp file and also in the
> topology file variable name which matches CHX. But still I am getting the
> same error.
> Kindly need help to resolve it.
Something doesn't add up. You will need to provide all of your files for
download via a file-sharing service to diagnose. A simple #include statement
and correct updating of [molecules] is all that is needed.
> On Fri, Sep 5, 2014 at 3:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 9/5/14, 2:50 AM, Christina Florina wrote:
>>> I have just started my work in MD and using Gromacs 5.0. I
>>> to use cyclohexane as my solvent instead of water. I generated the
>>> file, .itp and .gro using PRODRG. I have successfully incorporated the
>>> file using solvate command and generated the solvent box. But I am facing
>>> problem with grompp (ions.mdp) step before the addition of ions.
>>> gmx grompp -f ions.mdp -c protein_solv.gro -p protein.top -o ions.tpr
>>> I am getting the FATAL ERROR: NO SUCH MOLECULETYPE CHX
>>> I have checked with the molecule name (CHX) in the cyclohexane .itp file.
>>> have tired changing the name of the molecule also.
>>> Do I need to add this cyclohexane solvent molecule in the
>>> forcefield file or .atp file, .rtp file? I tried adding them but still not
>>> able to run this. I might be incorrect while adding it in the .rtp file.
>>> So, I kindly need help regarding the addition of new solvent
>>> molecule in gromacs since I have other organic solvents also for my md
>>> and having the same problem.
>> You need to #include the CHX .itp file in the system .top, and update
>> [molecules] accordingly. Please note as well that PRODRG topologies are of
>> low quality in my experience and need to be corrected. CHX is simple, a
>> ring of CH2 atom types, all with zero charge. Other results are less
>> trivial to fix.
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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