From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jun 27 2017 - 02:46:38 CDT
Hi Giacomo:
I am using for ABF the last frame (.xsc file) of MD equilibration
generated without PBCs enabled in NAMD config file. That config file only
had:
wrapNearest no
wrapAll on
If I measure directly the distance between the centers of mass of protein
and ligand for that frame:
> >Main< (francesco) 33 % set selprot [atomselect top "protein"]
> atomselect3
> >Main< (francesco) 34 % measure center $selprot
> 326.3038024902344 453.4432678222656 342.5987243652344
> >Main< (francesco) 35 % set sellig [atomselect top "segname SAA1"]
> atomselect4
> >Main< (francesco) 36 % measure center $sellig
> 329.97216796875 441.479736328125 317.9831237792969
>
>Main< (francesco) 37% set dist [veclength [vecsub [measure center
$selprot] [measure center $sellig]]]
27.613597797130065
>Main< (francesco) %
I get a result (27.6) different from "cv printframe" by loading that NAMD
frame to VMD (18.9).
Should any of these conditions be unsuitable for ABF, then, without a
complete reeducation, it will be difficult for me carrying out an ABF for
protein-ligand. However, I am strongly interested in that particular
protein-ligand system, I spend a lot of time in parameterizing the ligand.
I imagine that with FEP (not yet attempted) I'll be faced by samilar
problems.
francesco
On Mon, Jun 26, 2017 at 6:32 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Hi Francesco, when distances between groups of atoms are involved, it is
> really important to check that the PBCs are the same in both VMD and NAMD.
>
> Giacomo
>
> On Mon, Jun 26, 2017 at 12:24 PM, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> I also run the same ABF (rmsd all atoms of the ligand less methyl
>> hydrogens) with colvar "r" = 18.9 from cv printframe (unlike the directly
>> measured 27.6 with previous ABFs). In all cases, I took the colvars values
>> from the last frame of the 58.2ns MD, not averages along the whole
>> simulation)
>>
>>
>> Main< (Conformation:5xxf-SAA1) 28 % cv printframe
>>> 0 1.88926419197828e+01 5.22845307973583e+01
>>> -3.39612142392650e+01 9.26730407864645e+00 1.01135055762437e+02
>>> -5.05311208874754e+01 0.00000000000000e+00 0.00000000000000e+00
>>>
>>> >Main< (Conformation:5xxf-SAA1) 29 %
>>>
>>> >Main< (Conformation:Bound_5xxf-SAA1-allH_except_methyl_H) 33 % cv
>>> printframelabels
>>> # step r Theta
>>> Phi Psi theta
>>> phi RMSD r_RMSD
>>>
>>
>> The immediate (step 0) error was again atoms moving too fast, this time
>> one heavy atom and one H-atom of the ligand.
>>
>> f
>>
>> ---------- Forwarded message ----------
>> From: Francesco Pietra <chiendarret_at_gmail.com>
>> Date: Mon, Jun 26, 2017 at 12:28 PM
>> Subject: Fwd: Atoms too fast/periodic cell too small with ABF
>> protein-ligand
>> To: NAMD <namd-l_at_ks.uiuc.edu>
>>
>>
>> I must add that the attempted ABF was "Conformation:Bound". For rmsd for
>> the ligand I had chosen all heavy atoms.
>> By choosing all atoms of the ligand, except hydrogens at the methyl
>> groups, the simulation also crashed at the first step, this time for two H
>> atoms of the protein, one (HG1) very far from the ligand, the other one
>> (HA) close to the ligand.
>>
>> With "Conformation:Unbound" the ABF went to completion without errors.
>>
>> Hope this helps suggesting what to do.
>>
>> As I said, there was no problem with MD equilibration for this system, at
>> the same ts=1.0fs, along a trajectory of during 58.2ns.
>>
>> francesco
>>
>>
>> ---------- Forwarded message ----------
>> From: Francesco Pietra <chiendarret_at_gmail.com>
>> Date: Sun, Jun 25, 2017 at 12:56 PM
>> Subject: Atoms too fast/periodic cell too small with ABF protein-ligand
>> To: NAMD <namd-l_at_ks.uiuc.edu>
>>
>>
>> Hello:
>>
>> I am attempting a protein-ligand ABF, following the 2017 tutorial, by
>> using a 58.2ns problemless equilibrated system (ts=1.0 fs, bond restriction
>> on water only) in a TIP3P water box on a main pure-CPU cluster. Rather
>> large protein, organic ligand as accurately parameterized as I could, by
>> fitting torsions and water interaction.
>>
>> I am experiencing immediate "atoms moving too fast" (two H atoms of the
>> ligand) when using a linux 4-core cpu desktop, or "periodic cell has become
>> too small" on a linux GPU workstation. At the moment I have no access to
>> the cluster.
>>
>> I used ts=1.0 fs, i.e. no bond restriction, except for TIP3P water, as in
>> the equilibration.
>>
>> As a possible cause, that I was unable to verify, is the setting of Euler
>> and polar angle in the colvars definition. That is , I used the following
>> values from "cv printframe"
>>
>> >Main< (Conformation:5syf-SAA1) 28 % cv printframe
>>> 0 1.88926419197828e+01 5.22845307973583e+01
>>> -3.39612142392650e+01 9.26730407864645e+00 1.01135055762437e+02
>>> -5.05311208874754e+01 0.00000000000000e+00 0.00000000000000e+00
>>>
>>
>> by discarding the first two, and using the directly measured intercenter
>> distance of 27.6A in place of 18.89 from printframe, i.e., as follows:
>>
>>
>> harmonic {
>> colvars r
>> forceConstant 0.0
>> centers 27.6 # OK measured
>> }
>>
>>
>> harmonic {
>> colvars Theta
>> forceConstant 0.0
>> centers 52.3 # from printframe
>> }
>>
>>
>> harmonic {
>> colvars Phi
>> forceConstant 0.0
>> centers -40.0 # from printframe
>> }
>>
>>
>> harmonic {
>> colvars Psi
>> forceConstant 0.0
>> centers 9.27 # from printframe
>> }
>>
>>
>> harmonic {
>> colvars theta
>> forceConstant 0.0
>> centers 101.1 # from printframe
>> }
>>
>>
>> harmonic {
>> colvars phi
>> forceConstant 0.0
>> centers -50.5 # from printframe
>> }
>>
>> Should this assignment of colvars be correct, where to look for the
>> causes of the instability of the system?
>> I must confess that I am the first time at such an ABF beyond the tutorial
>>
>> Thanks for advice
>>
>> francesco pietra
>>
>>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>
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