Thanks Mark for the response.<br><br>I have contacted the amber mailing list too and I have got the parameters for GDP in AMBER94 forcefield. But I would need the parameters in AMBER03 forcefield, so that I can use them while running simulations in gromacs. So, can I use the same parameters of AMBER94 in AMBER03 too?<br>
<br>Neeru<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
On 10/12/2011 6:25 AM, neeru sharma wrote:<br>
> Dear gromacs users,<br>
><br>
> I have to simulate a protein-GDP complex using gromacs.As PRODRG was<br>
> giving unreliable output, I generated Amber topology and coordinate<br>
> files for GTP molecule. Then, I converted them into the corresponding<br>
> gromacs topology (.top) and coordinate files (.gro) and generated<br>
> parameter (.itp) file using following command (Thanks to Tsjerk):<br>
> sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e<br>
> '/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP<br>
><br>
> But the topology and co-ordinates file are quite different from the<br>
> input PDB file and hence the parameters are also faulty, the GDP<br>
> molecule is not fitting in the binding pocket of protein. Upon<br>
> tracking the whole process, it was found that the error might be while<br>
> using antechamber for generating prepin file using Gaussian output<br>
> file as the input.<br>
><br>
> Can anyone please suggest some way to apply some constraints in the<br>
> antechamber command itself. OR if anybody has the paramters or<br>
> topology for GDP, can anyone provide me the same so that I can compare<br>
> and see where the parameters are differing.<br>
<br>
Surely antechamber will accept whatever coordinate file you provide to<br>
it, and the AMBER mailing list is the place to make inquiries about it<br>
(after checking the documentation).<br>
<br>
Don't stress too much about the charges - those that are suitable in the<br>
bound and unbound form will normally be different, and current methods<br>
can't access the former.<br>
<br>
Mark<br>
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