VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Mar 21 2011 - 05:48:06 CDT

Hi Francesco,
The key question is, are the CHARMMGEN .inp/.rtf files correct? Either
they are wrong, or one of the assumptions that autopsf makes is invalid
for that structure and you need to change your settings. The best way to
check is to (a) manually inspect the .inp/.rtf files and make sure that
the atoms and connectivity match your expectations, and (b) try
generating the ibuprofen using psfgen instead of autopsf so that you
have finer control over what is being done to the molecule.

Best,
Peter

On 03/21/2011 06:12 AM, Francesco Pietra wrote:
> Hi:
> I wonder whether there is experience with coming to AUTOPSF with
> .inp/.rtf files generated for non-protein organic molecules with the
> AMBER10's tool CHARMMGEN. The web is silent to this concern.
>
> I am in trouble with ANTECHAMBER-CHARMMGEN for complex non-proteic
> ligands. Thererore, I tried with a simple ligand, ibuprofen. Using .ac
> type files (not .mol2 which caused immediately troubles to CHARMMGEN)
> from ANTECHAMBER, CHARMMGEN generated .inp/.rtf files that were
> accepted as topology by AUTOPSF, getting .psf/.pdb. AUTOPSF counted 34
> atoms, which I corrected to 33, as they are. However, loading these
> files to VMD, bond connections appear heavily altered. No more
> ibuprofen.
>
> Uncertain whether problems arising from my skipping PARATOOL (I am no
> GAUSSIAN owner) can be posted here, to avoid overloading the mailing
> list, I am not attaching files here. However, I would be happy to do
> that if there is interest (or kindness to help)
>
> Thanks
>
> francesco pietra