[gmx-users] Re: Problem on processing proteins consisting of two chains

[Spiwok Vojtech]

> Dear all,
>   I am a new user of Gromacs.I am trying to do a simulation on a protein
> which consists of two chains(A and B) like HIV PR.Unfortunately, the two
> chains got far away from each other. I found that two itp
> files(protein_A.itp and protein_B.itp) were generated after using pdb2gmx.
> It seems that Gromacs recognizes the two chains as different proteins,but
> they belong to the same molecule indeed.

Was the minimization or dynamics done in a solvent ?
If not, this could be also result of unfavourable contact between
atoms of each monomer that could result to spliting of dimer. I would
either solvate the dimer before the minimization or do some
re/constrained minimization or dynamics first.
 
>   How can I resolve the problem? Your experiences on Gromacs will helful
> for me.
>

Vojtech Spiwok
ICT Prague