[gmx-users] Problem with GDP parameters generation

[Mark Abraham]

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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