[gmx-users] monomer's conectivity

Andrea Muntean andreamuntean at gmail.com
Thu Oct 23 09:25:25 CEST 2008

Thank you for your answer.

If I am looking at the PDB standard format and my file, I observe that I
have only one number between the type of residue and coordinates, and I
suppose it is the residue current number. I am indeed missing the chain
identifier code, which should be of A1 Fortran format, which I don't really
understand (one carachter, but I have 32 chains, so it should be minimum A2
or I2). That I could introduce.
In my pdb entries I dont define any connectors. Should they be a dummy atom,
with the corresponding bond, angle, dihedhral, which after that I redefine
in the tdb file?
I dont think it is a visualisation artefact, because it really gives less
number of bonds, corresponding to the missing intermonomeric bonds.

Should I do now both (introducing a chain identifier in the pdb, but how?,
and defining the intermonomeric bonds via dummy in the pdb and tdb?)?

Thanks again for your help.

Best regards,
2008/10/22 Mark Abraham <Mark.Abraham at anu.edu.au>

>  Andrea Muntean wrote:
>> I have a *pdb file for a polymer box which I want to use. I defined the
>> residues (the first, the last and the inner monomers).
>> Pdb2gmx runs, but I obtain a "soup" of monomers instead of N chains a M
>> monomers each.
>> My problem now is how to connect the monomers. What is the best way to do
>> so?
> We can't tell yet. You might have a PDB file with each residue in its own
> chain. You might have defined residue topologies without suitable
> connectors. You might be observing a visualization artefact. You might have
> some warnings from pdb2gmx you haven't observed yet.
> Mark
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