On 11/12/2011 1:09 AM, neeru sharma wrote:
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?
Probably not, but you should go and read the papers in which the
development of each was described and make your own judgement. The
availability of parameters can be a sound reason for the choice of force
field.
Mark
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
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