[gmx-users] build membrane system from Charmm-Gui

Justin Lemkul jalemkul at vt.edu
Tue Aug 26 18:29:27 CEST 2014

On 8/26/14, 10:59 AM, Xiang Ning wrote:
> Dear Justin,
> Thanks a lot! I am looking forward to the new version CHARMM-GUI. However, at
> this moment, I was trying to put a protein inside the membrane. I used "editconf
> -f protein.pdb -o conf.pdb -box (my box demension x y z)" and then "genbox -cp
> conf.pdb -cs lipid_water_ion.pdb -o box.pdb" to remove the overlapped lipids. It
> looks fine in VWD, no overlap between protein and lipids occurred. However, when
> I try to generate top file by using " pdb2gmx -f box.gro -p box.top", It showed
> it did not know "K" (potassium). So I change all "K" to origin Charmm version
> "POT" in box.gro file, it can generate top file this time, but when I ran
> "grompp -f minim.mdp -c box.gro -p box.top -o box.tpr", it showed "Unknown cmap
> torsion between atoms 319 321 323 338 341".  I downloaded the patch
> "0001-Fix-pdb2gmx-merge-cmap.patch" to fix the problem, but it did not work (it
> asked file to patch which I don't know which file to patch). I would like to
> know, how to ran energy minimization in this case (protein inside the lipid
> membrane)? I used charmm36 force field for all atom by the way.

I have no idea what that patch script is or what it does.  The bigger question 
is what are those atoms, and why did pdb2gmx write a CMAP entry for them?


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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