VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Mar 21 2011 - 19:11:35 CDT

On 03/21/2011 08:20 AM, Francesco Pietra wrote:

> 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.

It is whatever type the atom has in the topology information that you
gave it. If you didn't give it a file that stores atom types, it would
be the atom name. What file did you get the topology information from?

Peter

>
> 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,
> C.ar for aromatic carbon,
> H for all hydrogens, either at aliphatic carbons or OH
>
> Thanks
> francesco
>
>
>
> 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
>>