[gmx-users] Unable to make .gro file
T.A.Wassenaar
T.A.Wassenaar at rug.nl
Fri Jun 3 09:14:53 CEST 2005
Hi Jeff,
pdb2gmx isn't a magic program to process anything right to
gromacs. It can only process chains of specified building
blocks. To get a topology for a molecule like this, you
can try the prodrg server
(http://davapc1.bioch.dundee.ac.uk/programs/prodrg/), but
don't expect too much of that either, since it's a bit of
a complicated structure you have there.
Hope it helps,
Tsjerk
On Fri, 3 Jun 2005 11:56:45 +0800
Jeffrey Chua <chuademon at gmail.com> wrote:
> Dear Friends,
>
> Hi! Im Jeff Chua, a new user to gromacs... I've been
>trying to do a md run
> on a dimer of beta carrageenan but whenever i try to
>produce a .gro and a
> .top file out of the given pdb file (using pdb2gmx_d
>since I dont have
> the pdb2gmx) the following error message is given.
>
> Processing chain 1 (80 atoms, 34 residues)
> Opening library file
>/home/apps/gromacs/share/top/specbond.dat
> 5 out of 5 lines of specbond.dat converted succesfully
> There are 0 donors and 18 acceptors
> There are 0 hydrogen bonds
>Fatal error: Residue 'CT' not found in residue topology
>database
>
> [jchua,/usr/ahpc-data-2/home/jchua/gromacs/Sample
>Runs,11:39]$
>
> Looking at the produced files, I see that a .top file
>has been produced
> and it contains the following:
>
> [jchua,/usr/ahpc-data-2/home/jchua/gromacs/Sample
>Runs,11:42]$ ls
> #beta.top.1# BetaDimer.pdb KappaDimer.pdb beta.top
> [jchua,/usr/ahpc-data-2/home/jchua/gromacs/Sample
>Runs,11:42]$ cat
> beta.top
> ;
> ; File 'beta.top' was generated
> ; By user: jchua (733)
> ; On host: ahpc
> ; At date: Fri Jun 3 11:39:18 2005
> ;
> ; This is your topology file
> ; 80 61
> ;
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
>
> [jchua,/usr/ahpc-data-2/home/jchua/gromacs/Sample
>Runs,11:42]$
>
> Ive looked over the oplsaa files that comes with gromacs
>and it does
> contain CT atom types. Am I doing something wrong?? Im
>attaching also the
> pdb file for your reference on the matter. (I hope this
>doesnt flood your
> emails...if it does, I apologize)
>
> I hope you could help me on this... thank you and God
>Bless.
>
>
> Respectfully,
>
> Jeff Chua
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