[gmx-users] residue database
spoel at xray.bmc.uu.se
Tue Jul 6 16:17:08 CEST 2004
On Tue, 2004-07-06 at 00:19, Dinesh Pinisetty wrote:
> Hello everybody,
> When I copy the methanol.pdb to a seperate directory from the
> tutor directory in gromacs and try to create a topology(.top) and
> coordinate(.gro)files through 'pdb2gmx',(I was using ffG43a1(official
> distribution force field)) I am getting following error:
> WARNING: 'MeO' not found in residue topology database,trying to use
> FATAL error: Atom Me1 in residue MEBMT 1 not found in rtp entry with 14
> atoms while sorting atoms.
> I tried to enter the residue 'MeO' in ffG43a1.rtp but I do not have the
> (bonds,charge,charge groups, improper dihedrals etc)which I found out from
> the manual are required,now I cannot add this residue MeO in .rtp.
> Please suggest me an alternative to create .top and .gro files and by the
> way how are they created in the 'methanol' directory under tutor,because I
> found that they were present readily in tutor directory.
> I hope that someone will do the needful,Thanks in advance.
you have to do it manually. chapter 5 of the manual. or use prodrg.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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