One question:
how to add new complex topology file to the tleap to solvate system on the
further steps?
E.g using below script I've loaded my complex.pdb
source leaprc.ff99SB
source leaprc.gaff
complex = complex.pdb
but
check complex
resulted in the 34 errors (corresponded to the ligand atoms) indicating
that ligand parameters have not been loaded.
Should I include paramtop file to the tlep ? Could you provide me with the
full script including solvate commands?
Thanks,
James
2014-04-29 19:34 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> Dear David,
>
> thanks for suggestions. Indeed renaming GUA to LIG have been resulted in
> complex without any errors.
>
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 658 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CTYR 1
> LIG 1
> NGLU 1
> )
> (no restraints)
> Writing pdb file: sensor_gua.pdb
> Converting N-terminal residue name to PDB format: NGLU -> GLU
> Converting C-terminal residue name to PDB format: CTYR -> TYR
> Quit
>
>
> James
>
>
> 2014-04-29 15:54 GMT+04:00 David A Case <case.biomaps.rutgers.edu>:
>
> On Tue, Apr 29, 2014, James Starlight wrote:
>> >
>> > Then I've parametrize my ligand following tutorial obtaining cGMP for
>> its
>> > deprotonated (-1) form
>> > antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2
>> -nc -1
>> >
>> > > check GUA
>>
>> If "GUA" is cGMP, try giving it a different residue name. I think you are
>> seeing the effects of Amber thinking that GUA is the old name for what is
>> now
>> called DG.
>>
>> You could also edit your leaprc file (or a copy of it) to remove the
>> aliasing
>> of GUA to DG. The alias is there to try to help people with old-style
>> (PDB
>> version 2) PDB files.
>>
>> > FATAL: Atom .R<DG3 207>.A<O2' 35> does not have a type.
>>
>> My guess(!?!) is that the DG3 comes originally from GUA, as described
>> above.
>>
>> > Here you can see that new oxygen have been added to the last protein's
>> TYR
>> > aa
>>
>> That looks correct: you have a TER card following the TYR, which Amber
>> takes
>> to mean that the TYR should have a carboxylate group at the end.
>>
>> >
>> > Created a new atom named: O2' within residue: .R<DG3 207>
>>
>> Same problem as above. Of course, deoxy-guanine won't have an O2' atom,
>> and LEaP gets confused.
>>
>> I'm guessing some here, but it's certainly worth a try to change the
>> residue
>> names.
>>
>> ...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Apr 29 2014 - 10:00:05 PDT
