[gmx-users] Residue 'SIA' not found in residue topology database

[Mark Abraham]

Maik Goette wrote:
> Right, Mark
> 
> But do you think, deleting something is the way, how to do it? ;)
> Maybe it could be problematic, if this molecule is, what they want to
> simulate in the protein...

I agree with you in a general context. However, for a new user, I think
it more likely that they are just using a PDB file blindly and haven't
learned to consider and/or modify its contents, because they haven't
encountered this kind of pitfall with pdb2gmx previously. Also likely is
that they haven't yet considered whether they want this other molecule
in their simulation system. I'm sure that we agree that this question
should be considered seriously before using pdb2gmx :-)

> Kong, a first step (maybe nothing for Newbies, thats for sure) would be
> to make some QM-calculations with e.g. Gaussian or try Antechamber (?)
> from the AMBER-package. After calculating reasonable partial charges,
> you can try to get the LJ-Parameters and other stuff from existing
> FF-entries. How to build the FF-entries, i.e. mainly an RTP-entry, one
> can obtain from the manual.

Yes, that's sound advice :-)

Mark