Dear Justin, Sorry I missed the reply for yesterday. So the atoms are mostly from my peptide: 319: atom C of VAL, 321: N of ILE, 323: CA of ILE, 338, C of ILE, and one from lipid POPC: 341: atom N of POPC. I just used "pdb2gmx -f box.gro -p box.top" to obtain the top file of the whole system, which including water, protein, lipid and ions. It generated several itp file and one top file. The CMAP is in "box_Protein.itp", which included the itp file of protein and lipid. After that, I ran grompp, and then the problem "unknown cmap torsion" occurred. I think the torsion was because it can not tell apart the last peptide atom and the first lipid atom. Could you please let me know how to solve this problem? Thanks a lot!
Best, Ning On Wednesday, August 27, 2014 10:23 AM, Justin Lemkul <jalem...@vt.edu> wrote: 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: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-August/091771.html -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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
