[gmx-users] rtp entry

[David van der Spoel]

ASHWINI JAYAPRAKASH wrote:
> Hi Mark,
>  
> I have used pdb2gmx to create the topology file with the option of 
> -missing,also I have deleted the HEATOM that were there in the pdb file. 
> Will these be a problem later?
>  
> Now when I run grompp I am getting the error
>  
> "Atomtype 'opls_135' not found!" .............
>  
as you see there is a problem.

read chapter 5 of the manual. you may be combining different force 
fields in the wrong way, but you are not giving any useful information .

> Any suggestions highly appreciated..
>  
>  
> Thanks,
> Aj
>  
>  
> */Mark Abraham <Mark.Abraham at anu.edu.au>/* wrote:
> 
>     ASHWINI JAYAPRAKASH wrote:
>      > Hi Mark,
>      >
>      > I have changed the atom name in the co-ordinate file. Now I get
>     an error
>      > saying :
>      > Residue "pop" not found in residue database
>      >
>      > My co-ordinate file consists of protein, popc and sol. Do I have
>     to add
>      > the itp files of popc and sol to the rtp file.
> 
>     Only if you want pdb2gmx to recognise these types of residues. See
>     http://wiki.gromacs.org/index.php/topology_file or chapter 5.
> 
>     Mark
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-- 
David.
________________________________________________________________________
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://folding.bmc.uu.se
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