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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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