Also when you look at the parameters
13 C4 ( c3) 15 C5 ( c3) 18 N2 ( n) 22 C6 (
c) 0.5300 1.0000 0.0000 1.2000
2.0000
13 C4 ( c3) 15 C5 ( c3) 18 N2 ( n) 22 C6 (
c) 0.1500 3.0000 180.0001 1.2000
2.0000
13 C4 ( c3) 15 C5 ( c3) 18 N2 ( n) 22 C6 (
c) 0.5000 4.0000 180.0001 1.2
50 C13 ( c3) 52 C14 ( c3) 55 N4 ( n) 59
C15 ( c) 0.5300 1.0000 0.0000 1.2000 2.0000
* 50 C13 ( c3) 52 C14 ( c3) 55 N4 ( n) 59
C15 ( c) 0.0000 2.0000 0.0000 1.2000 2.0000*
50 C13 ( c3) 52 C14 ( c3) 55 N4 ( n) 59
C15 ( c) 0.1500 3.0000 180.0001 1.2000 2.0000
50 C13 ( c3) 52 C14 ( c3) 55 N4 ( n) 59 C15
( c) 0.5000 4.0000 180.0001 1.2000 2.0000
The dihedral energies wont be affected I guess.
On Thu, Jun 25, 2015 at 2:22 PM, Arun Srikanth <askforarun.gmail.com> wrote:
> 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 - 12:00:02 PDT
