Sorry, should be www.pharmacy.Manchester.ac.uk/bryce/Amber
On Saturday, 10 December 2011, Marc van der Kamp <marcvanderkamp.gmail.com>
wrote:
> Hi neeru,
> You can find parameters/topology (+ reference) at
www.bryce.pharmacy.Manchester.ac.uk/bryce/Amber
>
> Marc
>
> On Saturday, 10 December 2011, neeru sharma <neeru.bioinfo.gmail.com>
wrote:
>> Dear amber users,
>>
>> I have to simulate a protein-GDP complex. For this,I have generated Amber
>> topology and coordinate files for GDP molecule after preparing GDP.lib
and
>> frcmod.GDP.
>>
>> 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 superimposition of the
>> generated topology and coordinate file with the initial PDB input file,
>> they were not being superimposed).
>>
>> 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)
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Sat Dec 10 2011 - 03:30:03 PST
