[gmx-users] Problem with GDP parameters generation

[neeru sharma]

Dear gromacs users,

I have to simulate a protein-GDP complex using gromacs.As PRODRG was giving
unreliable output, I generated Amber topology and coordinate files for GTP
molecule. Then, I converted them into the corresponding gromacs topology
(.top) and coordinate files (.gro) and generated parameter (.itp) file
using following command (Thanks to Tsjerk):
sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e
'/^\s*\[\s*moleculetype\s*\]\s*$/,$p'
TOP > ITP

But the topology and co-ordinates file are quite different from the input
PDB file and hence the parameters are also faulty, the GDP molecule is not
fitting in the binding pocket of protein. Upon tracking the whole process,
it was found that the error might be while using antechamber for generating
prepin file using Gaussian output file as the input.

Can anyone please suggest some way to apply some constraints in the
antechamber command itself. OR if anybody has the paramters or topology for
GDP, can anyone provide me the same so that I can compare and see where the
parameters are differing.

Thanks

----
Neeru Sharma
Pune (India)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111210/fbf6f9cd/attachment.html>