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On 11/12/2011 1:09 AM, neeru sharma wrote:
<blockquote
cite="mid:CALmmuEw6HnjDqNovDc7AbJ5ir=0tZh3ZgATMZYuHCL-aLMQfPA@mail.gmail.com"
type="cite">Thanks Mark for the response.<br>
<br>
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?<br>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CALmmuEw6HnjDqNovDc7AbJ5ir=0tZh3ZgATMZYuHCL-aLMQfPA@mail.gmail.com"
type="cite">
<br>
Neeru<br>
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<br>
On 10/12/2011 6:25 AM, neeru sharma wrote:<br>
> Dear gromacs users,<br>
><br>
> I have to simulate a protein-GDP complex using gromacs.As
PRODRG was<br>
> giving unreliable output, I generated Amber topology and
coordinate<br>
> files for GTP molecule. Then, I converted them into the
corresponding<br>
> gromacs topology (.top) and coordinate files (.gro) and
generated<br>
> parameter (.itp) file using following command (Thanks to
Tsjerk):<br>
> sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e<br>
> '/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP<br>
><br>
> But the topology and co-ordinates file are quite
different from the<br>
> input PDB file and hence the parameters are also faulty,
the GDP<br>
> molecule is not fitting in the binding pocket of protein.
Upon<br>
> tracking the whole process, it was found that the error
might be while<br>
> using antechamber for generating prepin file using
Gaussian output<br>
> file as the input.<br>
><br>
> Can anyone please suggest some way to apply some
constraints in the<br>
> antechamber command itself. OR if anybody has the
paramters or<br>
> topology for GDP, can anyone provide me the same so that
I can compare<br>
> and see where the parameters are differing.<br>
<br>
Surely antechamber will accept whatever coordinate file you
provide to<br>
it, and the AMBER mailing list is the place to make inquiries
about it<br>
(after checking the documentation).<br>
<br>
Don't stress too much about the charges - those that are
suitable in the<br>
bound and unbound form will normally be different, and current
methods<br>
can't access the former.<br>
<br>
Mark<br>
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