Thanks Justin. I know that using -ignh will solve the problem. But I was
just curious because I got the same error message ("Fatal error: Atom HD1
in residue HIS 65 was not found in rtp entry HISE with 17 atoms while
sorting atoms. ") when I used OPLS, this time it was His 65.So I used -his option in pdb2gmx and got the following options to choose Which HISTIDINE type do you want for residue 65 0. H on ND1 only (HISD) #Works. total charge= -17.000 1. H on NE2 only (HISE) # Error 2. H on ND1 and NE2 (HISH) #Works. total charge= -16.000 3. Coupled to Heme (HIS1) #Works. total charge= -17.000 So shall I go ahead with any of the option except 1, or use -ignh? On Tue, Apr 30, 2013 at 3:33 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/30/13 2:59 AM, Nikunj Maheshwari wrote: > >> Dear all, >> >> I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o >> output.gro) >> >> I used 13. GROMOS 53a6 force field >> >> "Fatal error: >> Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms >> while >> sorting atoms. >> >> For a hydrogen, this can be a different protonation state, or it >> might have had a different number in the PDB file and was rebuilt >> (it might for instance have been H3, and we only expected H1 & H2). >> Note that hydrogens might have been added to the entry for the N-terminus. >> Remove this hydrogen or choose a different protonation state to solve it. >> Option -ignh will ignore all hydrogens in the input." >> >> So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu) >> >> I get the following options. >> >> Which GLUTAMIC ACID type do you want for residue 1 >> 0. Not protonated (charge -1) (GLU) >> 1. Protonated (charge 0) (GLUH) >> >> Both options give the same error as before. >> >> The same error occurs for HB1 as well. >> >> Will I have to edit the pdb or rtp file? Or any other suggestions? >> >> > Read the error message again; it tells you what to do. > > Consider what you're doing - you're supplying a united-atom force field > with an all-atom structure. The chosen parameter set doesn't have explicit > hydrogens on nonpolar groups. Hence pdb2gmx complains that you're giving > it atoms it doesn't understand. Use of -ignh solves this issue, which is > precisely what the error message is telling you. > > -Justin > > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
