Thanks. Apart from this, is is there some script that keeps my original hydrogens from Maestro?
> El 30/3/2016, a las 19:43, Tsjerk Wassenaar <tsje...@gmail.com> escribió: > > Hey :) > > -ignh does ignore the hydrogens in the input file. It builds those > hydrogens that are specified in the force field. For histidines, the > protonation state is determined from the possible hydrogen-bonded network, > but it is possible to assign specific states interactively, using the > option -his, or by specifying the residue name in the input file. > > Hope it helps, > > Tsjerk > > On Wed, Mar 30, 2016 at 4:42 PM, sun <sun.i...@gmail.com> wrote: > >> I think using -ignh does not "remove" hydrogens. Hence, you can use it. >> >> Sent from my iPhone >> >>> On 30-Mar-2016, at 6:04 pm, rajendra kumar <rjd...@gmail.com> wrote: >>> >>> Hi, >>> >>> As suggested above, use -ignh to ignore hydrogen atoms. To use a specific >>> Histidine, you may change residue name HIS to >> HIP(Amber)/HSP(Charmm)/HISH( >>> OPLS >>> ) or HID(Amber)/HSD(Charmm)/HISD( >>> OPLS >>> ) or HIE(Amber)/HSE(Charmm)/HISE( >>> OPLS >>> ) either in PDB file or interactively through pdb2gmx usng -his command. >>> >>> >>>> On Wed, Mar 30, 2016 at 12:27 PM, bio hpc <biohpc2...@gmail.com> wrote: >>>> >>>> Hi, >>>> >>>> we have created some protein pdb files with Maestro. When we try to un >> an >>>> MD simulation with gromacs, we get errors like: >>>> >>>>>> Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14 >> atoms >>>> >>>> I tried to find a solution and it seems that internal gromacs dictionary >>>> for hydrogens is different from the one from Maestro and other formats. >> It >>>> seems, from what I read, that one must convert all hydrogen types to >>>> Gromacs format. Is is there any script that can do this automatically? >>>> >>>> Of course, there is the option “ignore hydrogens”, but this would be bad >>>> for us, since we need some histidines in the binding site, and so on. >>>> >>>> Thanks, >>>> BIO-HPC >>>> >>>> >>>> >>>> -- >>>> 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. >>> -- >>> 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. >> -- >> 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. >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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. -- 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.