Hi I am using ffG43a1p by Graham Smith which already has a definition for SEP (phosphorylated Serine). Best Ambrish
On 8/3/07, Xavier Periole <[EMAIL PROTECTED]> wrote: > > > the phosphorilated Ser is not defined in the G43a1 force field. > > You must define it. See manual for instructiion. > > XAvier > > > I am trying to perform simulation of a phosphorylated protein (phos. on > a > > Ser residue). I am tring to use *ffG43a1p as my forcefield. > > When I add a phosphate to the Ser, modify SER to SEP and run pdb2gmx it > > gives me this : > > *** > > WARNING: atom HG1 is missing in residue THR 1 in the pdb file > > You might need to add atom HG1 to the hydrogen database of > residue > > THR > > in the file ff???.hdb (see the manual) > > > > > > WARNING: atom H is missing in residue SEP 2 in the pdb file > > You might need to add atom H to the hydrogen database of residue > > SEP > > in the file ff???.hdb (see the manual) > > > > ------------------------------------------------------- > > Program pdb2gmx, VERSION 3.3.1 > > Source code file: add_par.c, line: 221 > > > >Fatal error: > > Atom NE21 not found in rtp database in residue GLN, it looks a bit like > NE2 > > ------------------------------------------------------- > > > > *Same protein without the phosphate and OPLS forcefield does not throws > any > > error.I have checked my pdb file and there is no NE21 in that. > > If any one has done a simulation with a phosphorylated protein using > > **ffG43a1p, > > then a sample pdb file would be very helpful and appreciated.* > > * > > Best, > > *-- > > Ambrish Roy > > > > Graduate Student > > Bioinformatics Center > > University of Kansas > > 2030 Becker Dr > > Lawrence, KS 66047 > > ----------------------------------------------------- > XAvier Periole - PhD > > 1- Institute of Molecular Assemblies > City University of New York - USA > 2- Molecular Dynamics-Group > University of Groningen - The Netherlands > http://md.chem.rug.nl/~periole > ----------------------------------------------------- > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Ambrish Roy Graduate Student Bioinformatics Center University of Kansas 2030 Becker Dr Lawrence, KS 66047
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