That happens when amber forcefield is used, doesnt it?. I'm using Gromos96 54a7 ff.
On Sun, Sep 28, 2014 at 10:02 PM, Johnny Lu <[email protected]> wrote: > Sometimes the forcefield can not directly use the residue names of a pdb > file. > In Amber forcefield, a glycine at c-terminal should be 'CGLY' instead of > just GLY. > Similarly, there is 'NGLY'. And histidine of different protonation states > have different names. > Cysteine with and without disulfide bond can have different names. > Sometimes residues in the pdb file can have multiple positions. > > On Sun, Sep 28, 2014 at 10:45 AM, Mark Abraham <[email protected]> > wrote: > > > Hi, > > > > There are some suggestions at > > http://www.gromacs.org/Documentation/File_Formats/Coordinate_File > > > > Mark > > > > On Sun, Sep 28, 2014 at 4:35 PM, Nizar Masbukhin <[email protected] > > > > wrote: > > > > > Dear users, > > > > > > I'm going to simulate a protein. On the pdb file contents, it's said > that > > > this protein has two chains, and missing residues and atoms. when I try > > to > > > pdb2gmx, the error messages occured. It seemed due tue the missing > > residue > > > so that i got the message error. > > > My question is: How can I add missing resiudes and atoms to the pdb > files > > > so that i can use it? > > > > > > Thanks > > > -- > > > 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 [email protected]. > > > > > -- > > 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 [email protected]. > > > -- > 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 [email protected]. > -- Thanks My Best Regards, Nizar Medical Faculty of Brawijaya University -- 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 [email protected].
