updated:
I've checked bottom of the *.inpcrd and found unfinished file (this time
I've not obtained any errors from tleap during saving both topology and
coordinates using saveamberparm complex *.prmtop *.inpcrd ) :
-19.6220000 -20.4660000 -23.4850000 -23.7830000 -34.9700000 -23.5740000
-24.
alternatively *.inpcrd file made for the same system using Chimera's GUI
looks correct and all md run without problems with it
-1.8603000 -40.1806000 -25.3217000 -2.4459000 -23.3482000 -26.1323000
-1.6321000 -23.6999000 -25.7724000 -2.6754000 -22.6263000 -25.5479000
64.7160000 75.0900000 72.6290000 90.0000000 90.0000000 90.0000000
Finally when I've loaded solvated pdb made by Chimera (including ligand
parameters) for checking topology and saving results in new files (using
below script) I've obtained brocked *.inpcrd again.
source leaprc.ff99SB
source leaprc.gaff
loadamberparams ligand.frcmod
loadoff ligand.lib
complex = loadpdb xz.pdb
check complex
saveamberparm complex 22.prmtop 22.inpcrd
How it could be fixed?
James
2014-04-30 10:53 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 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
>>>>
>>>
>>>
>>
>
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Received on Wed Apr 30 2014 - 04:00:02 PDT
