VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Oct 04 2018 - 15:32:20 CDT

Hi Francesco,

Not a topotools user, so Josh's answer is probably more on topic. I'll just
add that if you *only* want to add bond/angle/dihedral terms with neither
modifications of 1-2/1-3/1-4 exclusions nor changes in atom types, etc,
then the much underappreciated "extraBonds" functionality in NAMD is far
and away the easiest thing to use.

HTH,
BKR

On Thu, Oct 4, 2018 at 3:45 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Francesco,
>
> If the only thing you are doing is adding a bond, topotools has the
> required machinery to alter the internal representation within VMD so that
> VMD will write a legal psf afterward that describes the new system. So
> something like:
>
> topo addbond 1 2
> topo guessangles
> topo guessdihedrals
> [atomselect top "all"] writepsf new.psf
>
> What topotools doesn't do (and that psfgen will), is change atomtypes and
> charges as specified in the patch residue (PRES) command. So sure, you can
> make topotools make the bond and guess the angles and dihedral terms that
> need to be added from the new bond. It will not, however, check to make
> sure that your charges/atomtypes make sense for the new chemistry.
>
> -Josh
>
>
> On 2018-10-04 09:18:15-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Hi Axel
> You suggested 8 years ago, in a different context,
>
>> francesco,
>>
>> this is the kind of task, the topotools plugin was written for.
>>
>> you can do: topo addbond <atom id1> <atom id2>
>> or: topo delbond <atom id1> <atom id2>
>>
>> to selectively add or remove bonds. there are similar
>> commands to add/delete angles and dihedrals that
>> go with this bond, too. or you can use the guessangle
>> guessdihedral commands to rebuild the angle/dihedral
>> lists from the bond topology.
>>
> May I as whether
>
> package require topotools
>
> etc....
>
> can be inserted into psfgen and used to create a bond between a C-atom of
> a ligand and CYS-N of a protein? All that in place of using
>
> PATCH ....
>
> related to a specific PRES.
>
>
> thanks
>
> francesco pietra
>
>