From: James Starlight (jmsstarlight_at_gmail.com)
Date: Thu Apr 10 2014 - 05:32:48 CDT
Dear all,
many thanks for suggestion! I've recognized the problem- it was resulted
from the coordinates of water molecules taken from my previous run which
I've included in new model. That time I've included coordinates only for 4
selected waters which have been moved inside the protein during initial md
run joining hbonds with some polar residues. Below you can find script
where such water have been modeled explicitly as the individual segment
along with the protein and ligand.
package require psfgen
resetpsf
topology top_crq_final.inp
topology top_all27_prot_lipid.inp
topology top_all36_na.rtf
pdbalias residue HIS HSE
segment A {
pdb hex.pdb
first NTER
last CTER
}
coordpdb hex.pdb A
guesscoord
segment B {
pdb ligand.pdb
first NONE
last NONE
}
coordpdb ligand.pdb B
segment C {
pdb water.pdb
first NONE
last NONE
}
coordpdb water.pdb C
patch CY35 B:430
regenerate angles dihedrals
writepsf start_22.psf
writepdb start_22.pdb
Careful examination of the psf indicated that this water have made
covalent bonds with surrounding protein's atoms :) How It could be
preventing ?
2014-04-09 19:20 GMT+04:00 Morgan, Brittany <Brittany.Morgan_at_umassmed.edu>:
> Hi James,
>
> I would check your structure using the PSF to make sure that you do not
> have any bonds that should not be present. That can make your energy
> minimization fail catastrophically. I seem to recall an issue like this
> when using autodock myself, but it has been a long time so I don't remember
> the details.
>
> The different minimization protocols shouldn't make that much of a
> difference, and if you successfully minimized your protein in the apo form,
> it is unlikely that your configuration file is the problem.
>
> Brittany
>
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of
> James Starlight [jmsstarlight_at_gmail.com]
> *Sent:* Wednesday, April 09, 2014 10:38 AM
>
> *To:* Namd Mailing List
> *Subject:* Re: namd-l: Problems with energy minimization
>
> Thanks for suggestion!
>
> Its strange but I've tried to reconstruct this system in several ways (
> using different initial conformations for docking as well as varying XYZ of
> system eventually obtaining the same effect.
> but as I realize energy minimization is the actual way to resolve such
> clashes :) In any way could someone tell me
>
> 1- How it possible to found such clashes if visualization did not provide
> useful evidence.
>
> 2- Please provide me with some typical minimization.conf file (just for
> minimization of water-soluble system). How I could chose between stereed
> and CG-like algorithms ?
>
> Thanks for help,
>
> James
>
>
> 2014-04-09 18:14 GMT+04:00 Subbarao Kanchi <ksubbu85_at_gmail.com>:
>
>> Dear James,
>> It means that you have bad contacts in you initial
>> structure. Reconstruct the initial system with out bad contacts.
>>
>>
>> Regards,
>> Subbarao Kanchi
>>
>>
>> On Wed, Apr 9, 2014 at 7:37 PM, James Starlight <jmsstarlight_at_gmail.com>wrote:
>>
>>> Dear Namd Users!
>>>
>>> I have problems of the simulation of my protein-ligand water-soluble
>>> system. First I've simulated apo form of my protein. Than I've took final
>>> conformation from that run and using autpdock I've placed ligand within the
>>> protein's interior re-solvable my system and run energy minimization. This
>>> minimization run produced errors like ( I've used such conf file for any
>>> other systems taking it from the Namd tutorial and have not any problems):
>>>
>>> MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM DUE TO POOR PROGRESS
>>> LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
>>> PRESSURE: 6 -nan -nan nan nan -nan nan nan -nan -nan
>>> GPRESSURE: 6 -nan -nan -nan -nan -nan -nan -nan -nan -nan
>>> ENERGY: 6 9999999999.9999 9999999999.9999 9999999999.9999
>>> 9999999999.9999 9999999999.9999 9999999999.9999 0.0000
>>> 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999
>>> 9999999999.9999 0.0000 9999999999.9999 9999999999.9999
>>> 1065900.0000 9999999999.9999 9999999999.9999
>>>
>>> MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM DUE TO POOR PROGRESS
>>> LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
>>>
>>> I've tried to run it on gpu and cpu namd version but result was the
>>> same. How it could be fixed ?
>>>
>>>
>>> Thanks for help,
>>>
>>> James
>>>
>>
>>
>
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