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 below error
|
Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
peek_ewald_inpcrd: SHOULD NOT BE HERE
how I can easily obtain box vectors and include it to the inpcrd ?
James
2014-04-30 10:52 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> 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
