[gmx-users] Problem with GDP parameters generation

[neeru sharma]

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
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