Re: rmsd colvars atom definition

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Apr 10 2020 - 05:33:54 CDT

Hi Jerome
Most unfortunately I forgot saying that I am dealing with a system of an
organic (nonbonded) ligand in a receptor made of nucleosides. There is no
"CA" atom.

Minimization was OK except for the key distance between a CL-atom of the
ligand and N1 of one of the nucleosides, which was made too long. QM-MM OPT
with the best dispersion corrected functionals seems to be unable to
restore the correct halogen-pi distance, not surprisingly as QM-MM is faced
with a bad structure, where CL lies too far for feeling the pi-system.

Heating the minimized with a single distance colvars CL-N1 brought such
distance in order, however at the expense of the whole ensemble, which was
too much distorted.

Therefore, as N1 is present in all nucleosides, I tried rms colvars with
<atomNameResidueRange N1 residues> as reported above. The result was
disappointing: CL-N1 turned out to be somewhat shortened - which could be
enough - however at the expense of unacceptable distortion of the whole
ensemble. This is the reason for asking whether with rmsd colvars I can
define more atoms, or whole residues.

Thanks also for the vmd dashboard, of which I was unaware. May I ask
whether setting several distance colvars from the ligand to all nucleosides
could be a more promising approach than rmsd colvars? May aim is to arrive
at a compromise structure in which all halogen-pi and pi-pi stackings are
within a sensible distance, which might be optimized by QM-MM with
dispersion corrected functionals

All the best
francesco
I wish I could go back to the beautiful days when I was at the Station
Marine d'Endoume

On Fri, Apr 10, 2020 at 10:04 AM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Hi Francesco,
>
> if you are trying to select the C alpha, I assume their name is CA. What
> is N1?
>
> There is so far no way to select by residue name, however for that kind of
> task I'd recommend preparing the input using the Dashboard in VMD.
>
> Best,
> Jerome
>
> On Fri, 10 Apr 2020 at 09:56, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> Hello
>> I am looking for advice on defining <atomNameResidueRange> for rmsd
>> colvars. As shown below, I could define one atom only. To this concern, I
>> tried also <atomNameResidueRange P N1 2820-2821>
>> which was not accepted.
>>
>> Moreover, is it possible to define residue names in place of atom names?
>>
>>
>>> colvar {
>>> name colvar1 # needed to identify the variable
>>> lowerBoundary -2.0
>>> upperBoundary 2.0 ;# force will kick in when rmsd exceeds 2 A
>>>
>>>
>>> lowerWall -1.5 ;# a lttle higher than lowerBoundary
>>> upperWall 1.5 ;# a little lower than upperBoundary
>>>
>>> lowerWallConstant 100.0 ;# force constant in kcal/mol
>>> upperWallConstant 100.0
>>> outputTotalForce yes # reports also colvar system force
>>>
>>>
>>> rmsd {
>>> atoms {
>>> # add all the C-alphas within residues 2820-2821 of segment AN7
>>> psfSegID AN7
>>> atomNameResidueRange N1 2820-2821
>>> }
>>> # refPositionsFile sphere20_CEA_box_ion.pdb
>>> }
>>> ref PositionsCol X, Y, Z
>>> }
>>>
>>> colvar {
>>> name colvar2 # needed to identify the variable
>>> lowerBoundary -2.0
>>> upperBoundary 2.0 ;# force will kick in when rmsd exceeds 2 A
>>>
>>> lowerWall -1.5 ;# a lttle higher than lowerBoundary
>>> upperWall 1.5 ;# a little lower than upperBoundary
>>>
>>> lowerWallConstant 100.0 ;# force constant in kcal/mol
>>> upperWallConstant 100.0
>>>
>>> outputTotalForce yes # reports also colvar system force
>>>
>>>
>>> rmsd {
>>> atoms {
>>> # add all the C-alphas within residues 2869-2875 of segment AN8
>>> psfSegID AN8
>>> atomNameResidueRange N1 2869-2875
>>> }
>>> refPositionsFile sphere20_CEA_box_ion.pdb
>>> }
>>> # refPositionsCol X, Y, Z
>>> }
>>>
>>> harmonic {
>>>
>>> name AN7_harmonic
>>>
>>> colvars { colvar1 }
>>>
>>> centers 0.0
>>>
>>> forceConstant 10.0
>>> }
>>>
>>> harmonic {
>>>
>>> name AN8_harmonic
>>>
>>> colvars { colvar2 }
>>>
>>> centers 0.0
>>>
>>> forceConstant 10.0
>>> }
>>>
>>
>> Thanks
>> francesco pietra
>>
>

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