On 9/9/14 12:51 AM, Christina Florina wrote:
Hi,
I have included the link to my dropbox where I have attached my
gromacs topology files. Though I have included the cyclohexane itp file in
the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO,
Kindly need help in this regard.
Thank you in advance.
https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0
You have several problems:
1. The #include statement for chx.itp is probably wrong (though I don't know how
you're organizing your files), but unless you've put chx.itp in the force field
directory, #include "gromos43a1.ff/chx.itp" is incorrect.
2. The contents of chx.itp are wrong for several reasons. The #ifndef lines are
nonsensical and need to be deleted. The #include statement for water needs to
be deleted. The [system] and [molecules] levels (which are system-level and
thus can only go in a .top) need to be deleted.
-Justin
On Fri, Sep 5, 2014 at 5:25 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/5/14, 7:10 AM, Christina Florina wrote:
Hi,
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.
-Justin
On Fri, Sep 5, 2014 at 3:37 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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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==================================================
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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send a mail to gmx-users-requ...@gromacs.org.
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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