[gmx-developers] coordinate translation

[Ranjit Sudhakar Ranbhor]

hi,

I want to use gromacs for studying enzyme substrate complex. I obtained
substrate topology file from PRODRG server. I included the .itp file of
the substrate in enzyme's topology file and edited the .gro file of enzyme
by copying the coordinates of the substrate .gro file to enz.gro file. I
could energy minimize the system. But the problem is that the sustrate is
far away from active site. I want to bring substrate's coordinates near to
the active site of the enzyme. Is there any option in editconf
for translating the coordinates? I tried distance restraints (between one
active site atom and one substrate atom) but it is giving error saying

Atom index (2837) in distance_restraints out of bounds (1-2836)

where 2837 is the substrate atom and 2836 is enzyme's atom number.

I wonder if there is any way to solve this problem.

Regards,
Ranjit Ranbhor

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Ranjit Sudhakar Ranbhor
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Research Scholar
Biotechnology Centre
Indian Institute of Technology-Bombay
Powai, Mumbai-400 076.
India.
Tel: (91)-(022)-25764780 (Internal: 4780)
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Web site:http//www.btc.iitb.ac.in/~ranjit
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