Thanks!! :) now works!
2012/9/20 Justin Lemkul <jalem...@vt.edu>: > > > On 9/20/12 4:24 AM, menica dibenedetto wrote: >> >> Dear all, >> I have a problem with pdb2gmx function. >> I want to create the gro file of an acetylated at N-term protein. >> I copy here the head of the file: >> ATOM 2016 HC ACE 0 24.770 -62.381 -11.080 >> H >> ATOM 2015 CT ACE 0 25.644 -61.867 -10.739 >> C >> ATOM 2017 HC ACE 0 26.283 -61.657 -11.571 >> H >> ATOM 2018 HC ACE 0 26.167 -62.480 -10.034 >> H >> ATOM 2013 C ACE 0 25.231 -60.546 -10.063 >> C >> ATOM 2014 O ACE 0 24.058 -60.199 -9.966 >> O >> TER >> ATOM 2019 N MET 1 26.336 -59.728 -9.542 >> N >> ATOM 2020 H MET 1 27.236 -59.762 -9.976 >> H >> ATOM 1 CA MET 1 26.144 -59.704 -8.063 >> C >> >> The problem is that the output error told me that the atoms labels of >> ACE not correspond to the labels in the rtp file, >> but I checked it and them corresponds: >> Program pdb2gmx_d, VERSION 4.5.5 >> Source code file: pdb2gmx.c, line: 655 >> Fatal error: >> Atom HC in residue ACE 0 was not found in rtp entry ACE with 6 atoms >> while sorting atoms. >> >> I used the amber99sb-ildn.ff >> >> What can I do? > > > You've confused atom name with atom type. Refer to the aminoacids.rtp file > for the force field. I would also suggest removing the "TER" from between > the ACE and MET, otherwise pdb2gmx is likely going to try to write them as > separate chains. > > -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 > > ======================================== > -- > 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 -- 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
