VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Mar 22 2011 - 11:21:42 CDT

On 03/22/2011 12:03 PM, Francesco Pietra wrote:
>
> As "manually renaming" is appealing for the case in point, what do you
> mean exactly? Renaming the starting RIB.pdb at position 13-14 with c3,
> os oh ho (i.e., the atom names in the topology RIB.rtf), or their
> uppercase equivalent, is not what works. Should I rename both RIB.pdb

c3, os, etc. are the *types*, not the *names* -- see the topology file
tutorial if you're unclear on the distinction. The names are unique
identifiers (within a residue) for each atom. You need to name your
atoms C, C1, C2, etc. such that those names match up with the atom names
in the topology file.

I almost guarantee that one of antechamber's intermediate or final files
will have the atoms already so named; probably you can get it to spit
out a mol2 file, which vmd can read. This would save you the trouble and
possible error in manually assigning all of those names.

Best,
Peter

> and the topology RIB.rtf with atom names agreed by CHARMM ff? If so,
> either I find a recent list of atom names (I have one about which I am
> uncertain, a huge number of cases) or I should anyway draw the
> molecules with molefacture just to get the names and then carry out
> the manual renaming in the actual pdb. It seems that paratool would be
> a quicker approach (with more reliable partial charges).
>
> thanks
> francesco