VMD-L Mailing List

From: Vaidyanathan Sethuraman (vsethura_at_umn.edu)
Date: Thu Nov 23 2017 - 02:15:32 CST

Thanks Axel. autobonds no did the job.

Best Regards

Vaidyanathan M S

Postdoctoral Fellow
Kevin Dorfman's Group
Department of Chemical Engineering and Materials Science
University of Minnesota Twin Cities

On Wed, Nov 22, 2017 at 12:41 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
> On Wed, Nov 22, 2017 at 12:40 AM, Vaidyanathan Sethuraman <
> vsethura_at_umn.edu> wrote:
>
>> Dear VMD Users
>>
>> I am using Materials Studio to generate the initial structure for a
>> cellulose polymer. Then I export the PDB version to VMD and use topotools
>> to generate the input structure for LAMMPS. Please note that the PDB output
>> DO contain the CONNECT information (bond information).
>>
>> Q: Can I use topotools in such a way that it utilizes the CONNECT
>> information from PDB file while guessing angles and dihedrals rather than
>> using heuristics?
>>
>> When I use
>>
>> mol new inpfile.pdb autobonds yes waitfor all
>> topo guessangles
>> topo guessdihedrals
>> topo writelammpsdata out.data full
>>
>> the output still uses heuristics to compute "BONDS" and generates more
>> number of bonds than what is there in the CONNECT info. The reason why
>> heuristics is giving more bonds is because of the funky structure that some
>> atoms will look apparently close. So can I trick topotools in such a way
>> that the angle and dihedral topology is guessed from the CONNECT info?
>>
>
> ​this has nothing to do with topotools. topotools uses the information
> that VMD provides, which in turn depends on the PDB reader molfile plugin--001a114b6d06407fa1055ea20a83--