[gmx-developers] coordinate translation

[Anton Feenstra]

Ranjit Sudhakar Ranbhor wrote:
> 
> 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

editconf has several coordinate transformation options, e.g. 
-center <x> <y> <z> to set the center of a group of atoms at a
certain position. There may be other (non-Gromacs) programs, e.g.
molecular modeling packages, that are more suitable for this.

> 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.

Distance restraints are a molecule property (in Gromacs), and hence 
cannot be used between two separate molecules (i.e. enzyme and substrate).
There have been extensive discussions on the lists of workarounds.


-- 
Groetjes,

Anton
 _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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