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Hi Rashi<br>
<br>
To me, it seems more reasonable to use "pdb2gmx" for every molecule
that is supported by this utility (i.e. included in a rtp file) as
it will be more likely to be FF-compliant (at least for the default
rtp files) and thus compatible with your protein. PRODRG is, used
with some cautions, a very nice tool for kind of non-standard
ligands (as drugs) not included is such databases, but just for
them. <br>
<br>
If the starting PDB structure of your peptide is OK you would be
able to run "pdb2gmx" properly. Just try it and see<br>
<br>
Javier<br>
<br>
<br>
El 14/07/11 08:39, rashi parihar escribió:
<blockquote
cite="mid:CA+rLPkWVycAdyeAuE1-AK9MBdi-=71e_ftyXmf_=ZjN28CUmBw@mail.gmail.com"
type="cite">Hello everyone..<br>
I have to do the simulation of protein and peptide complex.I want
to ask as for protein and ligand complex we have to create
topology of ligand using prodrg sever mostly.Now if ligand is
peptide then I have to build the topology of peptide using
pdb2gx or anyother means?Looking forward 4r reply!! <br
clear="all">
<br>
-- <br>
<div> </div>
<div><span style="font-size: 24pt; color: rgb(255, 102, 0);
font-family: Wingdings;"><img alt="images[12]"
src="cid:part1.09010102.09070502@um.es" height="106"
width="99"></span></div>
<div> </div>
<div>“Many Smiles Begin Because Of Another Smile . . . ." <br>
<br>
Regards,<br>
Rashi</div>
<br>
</blockquote>
<br>
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