[gmx-users] Fwd: Need Help in Gromacs

[Balasubramani GL]

-------- Original Message -------- 

		SUBJECT:
 		Need Help in Gromacs

		DATE:
 		2014-03-05 16:47

		FROM:
 		Balasubramani GL <glbala87 at imtech.res.in>

		TO:
 		drbevan at vt.edu

Dear all, 

 We are simulating a few protein-ligand complexes by gromacs. For
parameter generation of non protein ligands we used prodrg server and
gromacs46a1 force field. We performed the PCA analysis. But strangely
the ligands are completely out of the protein molecule. Kindly suggest
some measures to treat this problem. 

Additionally we found that the in the tutorial mentioned on
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
for protein ligand the tutors have reassigned the charges and other
paramers for th ligand used in this tutorial following a paper below: 

PRACTICAL CONSIDERATIONS FOR BUILDING GROMOS-COMPATIBLE SMALL-MOLECULE
TOPOLOGIES

I request you to kindly send me a pdf copy of this paper. Also i will be
grateful to you if you can suggest something to solve the above
explained problem.

  

-- 
Thanks & Regards, 

G.L.Balasubramani
(Project-JRF),
c/o.Dr.S.Kumaran,
Structural & Quatitative Biology Lab, GNRPC,
Institute of Microbial Technology (CSIR),
Sector 39-A, Chandigarh, India-160036.
ph : +91-9876086625/9041280408 
off : 0172-6665475

-- 
Thanks & Regards, 

G.L.Balasubramani
(Project-JRF),
c/o.Dr.S.Kumaran,
Structural & Quatitative Biology Lab, GNRPC,
Institute of Microbial Technology (CSIR),
Sector 39-A, Chandigarh, India-160036.
ph : +91-9876086625/9041280408 
off : 0172-6665475