[gmx-users] Unknown cmap torsion between atoms

Justin Lemkul jalemkul at vt.edu
Wed Aug 27 16:17:14 CEST 2014

On 8/27/14, 10:14 AM, Xiang Ning wrote:
> Hi all,
> I was trying to put a protein inside the membrane (generated by Charmm-Gui and I made some modification). I used "editconf -f protein.gro -o conf.gro -box (my box demension x y z)" and then "genbox -cp conf.gro -cs lipid_water_ion.gro -o box.gro" to remove the overlapped lipids. It looks fine in VWD, no overlap between protein and lipids occurred, 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 try to built the box in several other ways, this problem kept occurring. So I searched for previous solution, and found the patch "0001-Fix-pdb2gmx-merge-cmap.patch" may fix the problem. However, I cannot use this patch because it needs to install in the source directory, but the Gromacs 4.5 I used is installed in our university system, I am not able to put the patch in the source directory.
> So I would like to know, can I put the patch in my work directory to make it work? It asked "file to patch" if I put it in my work directory, so which file I need to patch? Or are there any other method can solve the problem for "Unknown cmap torsion between atoms"? I used charmm36 force field for all atom by the way.
> Thanks very much for your attention and assistance!

See reply from yesterday:




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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