[gmx-users] Query regarding the addition of solvent molecule

[Justin Lemkul]

On 9/5/14, 2:50 AM, Christina Florina wrote:
> Hi,
>              I have just started my work in MD and using Gromacs 5.0. I need
> to use cyclohexane as my solvent instead of water. I generated the topology
> file, .itp and .gro using PRODRG. I have successfully incorporated the .gro
> 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  though
> I have checked with the molecule name (CHX) in the cyclohexane .itp file. I
> 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 work
> 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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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