Hello everyone, I' trying to simulate a system with multiple chains. According to the PDB entry, there is a single disulfide bond connecting two of the chains. Unfortunately, 'pdb2gmx' with '-ss' only allows formation of ss bonds within the same molecule.
I tried doing it manually via the following: (1) erase the hydrogens it added to the sulfur groups from the gro (after 'pdb2gmx') (2) re-numbering manually (by a script) the atom number (since i deleted two atoms) (3) connect the sulfur groups in the topology file (i.e. the itp files of each chain)
the first two part were easy, but once i changed the atom numbers in the gro file, i can no longer work with the itps because their atom number are now incorrect, and so i'm back to the starting point.
I saw this question on the GROMACS mailing list, however it was not fully answered:
https://www.mail-archive.com/[email protected]/msg50307.html
Looking at the GROMACS documentation at the following link: http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds
was not helpful either, because it only states what i'm already aware of.
There was a similar question in ReserchGate, and i followed some of the answers, but it didn't solve the issue.
Something tells me there must be an easier fix or perhaps i'm missing something. Thanks.
Dear Hila,
The easiest way to do this is by using the mechanism implemented with the specbond.dat file and pdb2gmx. You may find pdb2gmx -ss yes is useful. The sulfur atoms will need to be in the same unit that pdb2gmx is converting to a moleculetype, so invoking pdb2gmx -chainsep correctly may be required. See pdb2gmx -h. This requires that the two sulfur atoms be within a distance + tolerance (usually 10%) in order to be recognised as a disulfide. If your sulfur atoms are not this close, then either you can
- edit the contents of specbond.dat to allow the bond formation and do energy minimization very carefully to allow the bond to relax to a sensible length, or
- run a preliminary EM or MD with a distance restraint (and no disulfide bond) between these sulfur atoms with a large force constant so that they approach within the existing specbond.dat range to provide a suitable coordinate file for a second invocation of pdb2gmx.
Otherwise, editing your .top file by hand is the only option.
You can do it with the flag -chainsep. It will separate the chains and if the sulfur atoms are at the allowed distances, that is to say inside the cut-off, it will ask you to indicate whether the disulfide bridge exists or not with the flag -ss, or with -inter, where it will ask you about amino acid, carboxyl and amino terminal charges too.
Then, you need to check your file.gro (visualize it), because sometimes you need to eliminate the H atoms of SH groups interchain (HG of CYS).
Cheers
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