One question. After salvation of my protein:
Loading PDB file: ./sensor_gua_min.pdb
total atoms in file: 3209
Solute vdw bounding box: 50.809 61.239 56.112
Total bounding box for atom centers: 66.809 77.239 72.112
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 69.814 80.169 75.186 angstroms.
Volume: 420812.419 A^3
Total mass 203553.582 amu, Density 0.803 g/cc
Added 10024 residues.
Checking Unit.
any information of the PBC have been lost in the resulted *.inpcrd
(bottom line consist of only 4.7803570 value)
so the minimization in the explicit solvent end with the
2014-04-30 10:33 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> Jason,
>
>
> Thanks for suggestion. I've solved this issue by such modification of the
> charge in the ligand.lib (not mol2) file consisted of the ligand topology
> which I've used during complex preparation.
>
> James
>
>
> 2014-04-29 23:38 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
>
> On Tue, 2014-04-29 at 22:48 +0400, James Starlight wrote:
>> > Dear David,
>> >
>> >
>> > thanks for suggestions again.
>> >
>> > One question: what should I do with the non-integer charges (below you
>> can
>> > see warning obtained for my solvated system?)
>> >
>> > WARNING: The unperturbed charge of the unit: -2.998000 is not zero.
>> >
>> > In this case -2 charge came from the protein and ligand should have -1
>> as
>> > defined during its parametrization:
>> > antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2
>> -nc -1
>>
>> I suggest modifying ligand.mol2 and subtracting 0.002 from one of the
>> atoms with a bigger positive or negative charge.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 30 2014 - 00:00:04 PDT
