I have further analyzed the problem.
The dihedral count for one molecule is 102
The dihedral count for two molecules is 205 it should be 204
This is that dihedral. The second one should be repeated 3 times but it
appears four times in the topology file giving rise to an additional
dihedral.
13 15 18 22 3
50 52 55 59 4
I wonder why tleap would print an extra dihedral when there are two
molecules. Please look into this
Thanks
Arun Srikanth
On Thu, Jun 25, 2015 at 11:21 AM, Arun Srikanth <askforarun.gmail.com>
wrote:
> I have the mol2 file, frcmod for 2mol.pdb from antechamber from the
> following commands
> and the mol2,frcmod file for 1mol.pdb
>
> antechamber -fi pdb -fo mol2 -i 2mols.pdb -o 2mols.mol2
> parmchk -f mol2 - i 2mols.mol -o 2mols.frcmod
>
> tleap
> source leaprc.gaff
> sus=loadmol2 2mols.mol2
> loadamberparams 2mols.frcmod
> saveamberparm sus 2mol.top 2mol.crd
>
> close tleap
>
> second method
> tleap
> source leaprc.gaff
> sus1=loadmol2 1mol.mol2
> sus2=loadmol2 1mol.mol2
> sus=combine {sus1 sus1}
> loadamberparams 1mols.frcmod
> saveamberparm sus 2mol_combine.top 2mol_combine.crd
>
> If you count the dihedrals in from each of the topology files, the second
> one gives 206 and the first one gives 205 actually it should be 204 since
> the dihedrals from 1mol.top is 102.
>
> I have not checked the dihedral energies but there is inconsistency in the
> dihedral count
>
> Arun
>
>
> On Thu, Jun 25, 2015 at 8:22 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Wed, Jun 24, 2015, Arun Srikanth wrote:
>> >
>> > I am attaching the pdb file of the molecule I am working with (1mol.pdb
>> > file contains one molecule, 2mol.pdb contains 2 molecules).
>> > I need to get the amber topology file for 2mol.pdb
>>
>> We would certainly need to know the exact commands you gave to tleap to
>> create
>> the topology files.
>>
>> > I generated amber topology file for a mixture of two molecules in two
>> > ways.
>> >
>> > First:
>> >
>> > Create a pdb file of two molecules using packmol which is 2mol.pdb. Get
>> the
>> > topology file from amber.
>> >
>> > The number of dihedrals in this case is 205
>> >
>> > Second:
>> >
>> > With one mol2 file of the molecule use combine command in tleap to
>> generate
>> > the topology file
>>
>> Are the energies the same for the two cases? The "combine" command is
>> *very*
>> rarely used by Amber developers, so there could be problem there, I
>> suppose.
>> But we need more than just a qualitative description of what you did: we
>> need
>> the exact commands that you used.
>>
>> ...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Jun 25 2015 - 11:30:02 PDT
