[gmx-users] problem in protein - cofactor linkage

pankaj at cdfd.org.in pankaj at cdfd.org.in
Tue Jul 27 05:23:23 CEST 2004

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 ?

Waiting for your suggessions.

Thanking you,

Pankaj kumar.

pankaj kumar (phd student)
C/O Dr H.A.Najarajaram
Laboratory of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagonistic
ph.no 91-9848592448


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