[gmx-users] monomer's conectivity

Andrea Muntean andreamuntean at gmail.com
Thu Oct 23 13:37:23 CEST 2008

Thank you. I hope this helps me further.
My system is 32 polystyrene chains of 80 monomers.
2008/10/23 Mark Abraham <Mark.Abraham at anu.edu.au>

> Andrea Muntean wrote:
>> 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.
> Get a PDB file with just one polymer molecule and work on getting a
> topology for that. Walking before running :-)
> 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?
> First you need a functional *residue topology*. Check chapter 5 of the
> manual and look at the other force fields to see how (for example) protein
> force fields define the connectors with + and - prefixes. Once you've got
> that, then it's possible for pdb2gmx to join them head to tail (using the
> residue number field to indicate the breaks, and the name to match up with
> the topology you've defined), and you may then need either terminating
> residues of a different name or a .tdb entry.
> I dont think it is a visualisation artefact, because it really gives less
>> number of bonds, corresponding to the missing intermonomeric bonds.
> Your visualization software is not reading a file format that is encoding
> any topology (since you haven't produced one yet). Thus it's inventing some
> bonds based on the coordinates. The output of pdb2gmx that contains topology
> information is the .top file, not the coordinate file.
> 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?)?
> I suppose there are some circumstances where chain identifiers might be
> useful, but since you haven't even told us what your monomer and system are,
> it's hard to help you.
> Mark
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