From: Francesco Pietra (
Date: Mon Mar 21 2011 - 07:20:00 CDT

sorry, forgot the list

---------- Forwarded message ----------
From: Francesco Pietra <>
Date: Mon, Mar 21, 2011 at 1:18 PM
Subject: Re: vmd-l: charmmgen to autopsf
To: Peter Freddolino <>

On Mon, Mar 21, 2011 at 11:48 AM, Peter Freddolino <> wrote:
> 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

Hi Peter
could you please give a web reference for a list of atom types that
VMD indicates with Mouse > Query ? I mean also for organic molecules.

The list I have of CHARMm atom types (don't know the origin)  does not
correspond to VMD. Must be a wrong list. For ibuprofen I get from VMD:
C.2 for carbonyl carbon,
O.2 for carbonyl oxygen,
O.3 for -OH,
C.3 for aliphatic carbon, for aromatic carbon,
H for all hydrogens, either at aliphatic carbons or OH


 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