On Fri, Nov 9, 2012 at 12:20 PM, Justin Lemkul <[email protected]> wrote: > > > On 11/9/12 5:27 AM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I used pdb2gmx to generate topology of the new molecule of which >> parameters I added to ffbonded.itp and aminoacids.rtp creating new >> resiude: >> >> pdb2gmx -f LIG.pdb -o LIGproc.pdb -p topol.top >> >> Back Off! I just backed up topol.top to ./#topol.top.1# >> Processing chain 1 'X' (49 atoms, 3 residues) >> There are 0 donors and 0 acceptors >> There are 0 hydrogen bonds >> Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA. >> Warning: Starting residue LIG2 in chain not identified as Protein/RNA/DNA. >> Warning: Starting residue FE3 in chain not identified as Protein/RNA/DNA. >> Problem with chain definition, or missing terminal residues. >> This chain does not appear to contain a recognized chain molecule. >> If this is incorrect, you can edit residuetypes.dat to modify the >> behavior. >> 8 out of 8 lines of specbond.dat converted successfully >> Opening force field file ./charmm27mod.ff/aminoacids.arn >> Opening force field file ./charmm27mod.ff/dna.arn >> Opening force field file ./charmm27mod.ff/rna.arn >> Checking for duplicate atoms.... >> Now there are 3 residues with 49 atoms >> Making bonds... >> Number of bonds was 46, now 46 >> Generating angles, dihedrals and pairs... >> Before cleaning: 114 pairs >> Before cleaning: 114 dihedrals >> Keeping all generated dihedrals >> Making cmap torsions...There are 114 dihedrals, 2 impropers, 76 >> angles >> 114 pairs, 46 bonds and 0 virtual sites >> Total mass 446.147 a.m.u. >> Total charge -0.000 e >> Writing topology >> >> Back Off! I just backed up posre.itp to ./#posre.itp.1# >> >> Writing coordinate file... >> >> >> >> Then when i try to process to grompp: >> >> grompp -f minim.mdp -c LIGp.pdb -p topol.top -o em.tpr >> >> An input file contains a line longer than 4095 characters, while the >> buffer passed to fgets2 has size 4095. The line starts with: '20s' >> >> I cannot get rid of this. When I process without topology of the new >> molecule (e.g. processing protein with pdb2gmx and then grompp) >> everything is fine. It is not the fault of gurgle.dat, installation of >> Gromacs (I tried on 3 machines) surely. I also checked lenght of lines >> in topol.top, everything is fine. >> >> Please, advise, I loose my time :( >> > > You probably have some unrecognized line break in one of the files. Try > dos2unix. > > -Justin
I do this every time after generatin each file. It does not help. Would you kindly try to process grompp using my files? > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
