sunny mishra wrote:
Hi Johny and Justin,
Thanks for the reply. But another problem here arises regarding the
1K4C_clean.top file. I have to minimize the system in vacuum i.e.
without adding any water molecules in it. After making the .gro file
from 1K4C_clean.pdb file with the help of genbox command and when I do
the grommp command it says that your .gro file does not match with the
.top file. But I can get rid of that by adding W molecules. It doesn't
If you have to add waters to make the .gro match the .top, then water molecules
have been added to the [molecules] section in the .top. The real solution is to
fix the [molecules] section to actually do an in vacuo minimization.
-Justin
make sense to me that when I am trying to minimize the system in vacuum
why do I have to add the water molecules or add anything else. They
should match...do you guys have any idea? Also, in my .top file I am
using the martini.itp file and also 1K4C_clean.itp file which I
generated from seq2itp.pl script after getting the .ssd files.
Sunny
On Tue, Aug 18, 2009 at 6:01 PM, Johnny Lam <[email protected]
<mailto:[email protected]>> wrote:
Hi Sunny,
Justin is right in saying that the hydrogen bonds will be absent in
the coarse grained file. For MARTINI, you would need to get the
secondary structure information from the original, un-CG .pdb file
(in your case, your 1K4C clean pdb file). When doing the topology,
it will become clear that the .ssd file that is required will be
that obtained from your original pdb file. That is how the MARTINI
force field works. I hope this helps!
Best,
--Johnny
--
-------------------------------------------------
Johnny Lam
ISPE Berkeley Chapter External Vice President
Department of Bioengineering
College of Engineering
University of California, Berkeley
Tel: (408) 655- 6829
Email: [email protected] <mailto:[email protected]>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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