Thanks Justin, I think that I have to write a script to remove hydrogens that are not suitable for united-atom forcefield. After this operation I can use pdb2gmx.
On Fri, Oct 29, 2010 at 10:05 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Deniz KARASU wrote: > >> Hi all, >> >> I'm trying to convert a protein, that is protonated with another special >> software and by manually checking, with pdb2gmx. I am using FF53A6 >> forcefield and don't use -ignh option. When I run pdb2gmx it gives me this >> error. >> >> Atom HA in residue VAL 1 not found in rtp entry with 8 atoms >> while sorting atoms. Maybe different protonation state. >> Remove this hydrogen or choose a different protonation state. >> Option -ignh will ignore all hydrogens in the input. >> >> I understand that the hydrogen atom is not defined in forcefield for VAL >> residue and need selection protonation state interactively. >> I wonder that there is anyway to convert protonated protein for specified >> forcefield (including united-atom ff) and assign automatically protonation >> state according to bonded hydrogen in structure? >> >> > You can't choose to ignore some H atoms while recognizing others. Either > you provide pdb2gmx with a suitable structure that can be used exactly by > the force field, or you let pdb2gmx assign protonation states after ignoring > all input H atoms. Fortunately, for all termini and titratable residues, > you can do so with the -ter and -inter options. > > -Justin > > Thanks. >> >> Deniz. >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 >
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