[gmx-users] Unable to make .gro file

[parinald at unsl.edu.ar]

Define your molècule in ffG43a1.rtp file and in aminoacids.dat (just only
the name), for example AGP-BGP
then you have to use pdb2gmx program.



>
> 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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