From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Oct 05 2018 - 12:00:09 CDT

Hi Brian and Jos:
Thanks for the comments. Actually, making a chemical bond usually modifies
atom types and charges, surely in my case of adding the NE2 N-atom of
histidine to a sp2 carbon of the ligand, with H-addition to the adjacent
sp2 carbon. I hoped in a tool that can be inserted into the psfgen
protocol. I understand that, for the time being, I have to set up from
scratch a specific PRES, hopefully with already existing atom types in the
labyrinth of CGenFF.
cheers
francesco

On Thu, Oct 4, 2018 at 10:32 PM Brian Radak <brian.radak_at_gmail.com> wrote:

> 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
>>
>>