[gmx-users] monomer's conectivity

[Mark Abraham]

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