[gmx-users] problem in protein - cofactor linkage

Anton Feenstra feenstra at chem.vu.nl
Tue Jul 27 09:51:10 CEST 2004

pankaj at cdfd.org.in wrote:

> Dear All,
> I am simulating a protein having PLP co-factor. PLP has a covalent linkage 
> with a lysine residue of the protein.
> I got the topology for the PLP from PRODRG server and included it as itp 
> file. But the covalent bond has not been formed. In the simulation the 
> cofactor moves away from the protein probably due to the non-existance 
> of the covalent bond interaction.
> Later I included a line in the specbond.dat file specifying the PLP-LYS 
> linkage and copied it into the working directory and ran the simulation. 
> Even this time the PLP has moved away from the protein, which means that 
> the covalent bond is not still formed.
> I feel that the specbond.dat entry will be read only when the residue type 
> of PLP is defined in the rtp file. Is this correct ?
> How can the covalent bond between the protein and PLP be made ?

That is right - pdb2gmx parses the specbonds while it builds your molecule
from rtp buildingblocks.

There are ways you could solve this:
1) convert the .itp file for PLP to an rtp entry. That isn't much work, it
    is mainly a matter of changing atom numbers into atom names and possibly
    rearranging some columns. There is a set of scripts 'Gromacs Topology tools'
    in the contributions section, nr2nametop is the one you could use.
2) Manually 'add' your PLP topology to the protein topology. Again you can
    use my top tools. First run nr2nametop on your PLP. Then add each of the
    [atoms], [bonds], [angles] section from PLP to the end of the correpsonding
    section of your protein. THen manually add the bond from PLP to protein,
    and finally run renumtop to change all atom labels back to atom numbers.

If your have problems using the scripts, ask me again. They generatlly work
# renumtop < merged.top > renumbered.top

(Come to think of it, it would not be difficult to make a script that merges
two (or more) topologies automatically...)


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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