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 <[EMAIL PROTECTED]>/* 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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