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On 10/12/2011 6:25 AM, neeru sharma wrote:
<blockquote
cite="mid:CALmmuEw0GhpiVxAHF0A6t3TgxZY6O3UvBXqSgdCAzcRFvMZEAQ@mail.gmail.com"
type="cite">Dear gromacs users,<br>
<br>
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 <span class="Apple-style-span" style="color: rgb(34,
34, 34); font-family: arial,sans-serif; font-size: 13px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
text-indent: 0px; text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px; background-color: rgba(255, 255,
255, 0.918); display: inline ! important; float: none;">Tsjerk)</span>:<br>
<span class="Apple-style-span" style="color: rgb(34, 34, 34);
font-family: arial,sans-serif; font-size: 13px; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
text-indent: 0px; text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px; background-color: rgba(255, 255,
255, 0.918); display: inline ! important; float: none;">sed -n
-e '/^\s*\[\s*system\s*\]\s*$/q' -e
'/^\s*\[\s*moleculetype\s*\]\</span><span
class="Apple-style-span" style="color: rgb(34, 34, 34);
font-family: arial,sans-serif; font-size: 13px; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
text-indent: 0px; text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px; background-color: rgba(255, 255,
255, 0.918); display: inline ! important; float: none;">s*$/,$p'
TOP > ITP</span><br>
<br>
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. <br>
<br>
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.<br>
</blockquote>
<br>
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).<br>
<br>
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.<br>
<br>
Mark<br>
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