Dear professors,
Thank you very much for all the feedback. Like it was said deletebond
would be a very helpful feature to my goal. I have one more question:
suppose that after delete the desired bond length, a charge redistribution
of -q over the target enzyme atom and +q over the target ligand atom is
desired. it would be also possible to do it by ParmEd.
Best whishes,
Hector.
> thanks, that's a very helpful feature. of course people should think about
> whether the remaining terms are still reasonable since it's a different
> molecule now. for example, should the atom types or partial charges
> change?
> I can imagine lots of cases where deleting a bond would be useful, but
> other cases where people should probably generate a new prmtop from
> scratch, depending on exactly what they are trying to learn. just adding
> that here in case people read the archives...
>
> On Thu, Sep 17, 2015 at 11:16 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Thu, Sep 17, 2015 at 9:48 AM, Carlos Simmerling <
>> carlos.simmerling.gmail.com> wrote:
>>
>> > Jason - correct me if I'm wrong, but if you delete the bond parameter,
>> it's
>> > true that it won't be there, but it won't delete the angle term
>> between
>> > atoms across the previous bond, or the torsion parameters. There is
>> also
>> > the problem of the nonbonded interactions. the atoms previously bonded
>> > won't have any nonbonded, nor will the 1-3 atoms, so these molecules
>> can
>> > float on top of each other near the deleted bond. I would imagine the
>> only
>> > good way to do this is to remove the bond before you make the prmtop,
>> not
>> > after... unless parmed is smarter than I thought!
>> >
>>
>> ​ParmEd is smarter than you thought ;). deleteBond does all of this.
>> It
>> deletes the bond in its entirety (including all other valence terms that
>> include that bond), and it always recomputes the exclusions before
>> writing
>> a topology file.
>>
>> All the best,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
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--------------------------------------
Dr. Héctor A. Baldoni
Profesor Adjunto
Departamento de Química
Área de Química General e Inorgánica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
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Received on Thu Sep 17 2015 - 11:00:08 PDT
