Thanks Mark for the response. 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?
Neeru > > On 10/12/2011 6:25 AM, neeru sharma wrote: > > 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. > > Surely antechamber will accept whatever coordinate file you provide to > it, and the AMBER mailing list is the place to make inquiries about it > (after checking the documentation). > > Don't stress too much about the charges - those that are suitable in the > bound and unbound form will normally be different, and current methods > can't access the former. > > Mark > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111210/8550a169/attachment-0001.html > >
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
