[gmx-users] Unable to make .gro file

[T.A.Wassenaar]

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