VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Mar 22 2011 - 13:38:37 CDT

Hi Peter:
Thanks for you guidance (and patience). It works now by manually
adjusting the atom names in the starting pdb. You said "names", I took
"types", although I know the difference. It should have not occurred.
Very sorry.
Have a nice evening.
francesco

On Tue, Mar 22, 2011 at 5:21 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> 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
>
>