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
>
>
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Received on Thu Jun 25 2015 - 08:30:02 PDT
