I have checked again .The problems is only with this molecule. I checked
with other molecules that I am working with. The sum of individual
dihedrals is equal to the number of dihedrals in the mixture.
I presently do not know why. Also I am still trying spot the additional
dihedral
Thanks
Arun
On Wed, Jun 24, 2015 at 6:13 PM, Arun Srikanth <askforarun.gmail.com> wrote:
> The problem occurs with one of the molecule (in the mixture). So I
> investigated this molecule separately.
>
> So for this molecule the total number of dihedrals 102.
>
> For two molecules (same molecule) the total number of dihedrals is 205.
>
> I am attaching the pdb files respectively.
>
> Please let me know as why there is an extra dihedral in topology file.
>
> Is this a bug ?
>
> Thanks
> Arun
>
>
>
>
>
> On Wed, Jun 24, 2015 at 5:26 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Wed, Jun 24, 2015 at 4:45 PM, Arun Srikanth <askforarun.gmail.com>
>> wrote:
>>
>> > Thanks. I have another question now.
>> >
>> > I am preparing a mixture of two molecules in the ratio of 3:2.
>> > I have the individual topology files of the molecules from tleap.
>> > I have also generated the topology file for the mixture(3:2) from tleap
>> > The number of dihedrals for the mixture is 685 (including impropers).
>> The
>> > individual number of dihedrals are 160 and 102 for each of the
>> molecules.
>> > Now for 3:2 ratio the total number of dihedrals should be 684 (3x160
>> > +2x102). However I am getting one dihedral extra from the topology file
>> of
>> > the mixture.
>> >
>> > Why is this so ?
>> >
>>
>> No clue. Any idea *what* the extra dihedral term is? If not, can you
>> send me the relevant files to try and reproduce this?
>>
>> Thanks,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
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>
>
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Received on Wed Jun 24 2015 - 16:30:02 PDT
