Fwd: ABF FEP with multichain receptor

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jul 11 2017 - 01:20:12 CDT

hello jerome:
Did you see the r colvar that I posted, and my doubt, now, whether "r"
should refer to the distance between the centers of mass of ligand and
protein or rather to the distance between the ligand and the protein
residues facing the ligand? What I get from "cv printframe" is a short
distance.

thanks
francesco
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sun, Jul 9, 2017 at 7:44 AM
Subject: Re: namd-l: ABF FEP with multichain receptor
To: Jérôme Hénin <jerome.henin_at_ibpc.fr>
Cc: Namd Mailing List <namd-l_at_ks.uiuc.edu>

Colvarstrajfrequency 100
Colvarsrestartfrequency 100

#############################################################
>> # rmsd PMF
>> # r, Theta, Phi, Psi, theta, phi UNRESTRAINED
>> # r and polar angles theta phi defining the position of ligand with
>> respect to protein
>> # Euler angles Theta Phi Psi define ligand orientation
>> #############################################################
>> # COLVARS DEFINITIONS
>> #############################################################
>>
>>
>> colvar {
>> name r
>>
>> width 1.0
>>
>> lowerboundary 0.0
>> upperboundary 40.0
>>
>> lowerwallconstant 100.0
>> upperwallconstant 100.0
>>
>> distance {
>> forceNoPBC yes
>> group1 {
>> atomnumbers : { 12258 12259 12260 12261 12280 12281 } # PROT
>> R359: N HN CA HA C O
>> }
>> group2 {
>> atomnumbers { 13439 13438 13437 13445 13446 13448 } # SAA1
>> hydrofuran: C2 C1 O1 C8 C9 C11
>> }
>> }
>> }
>>
>
ARG 359 faces the ligand atoms in group 2

On Sat, Jul 8, 2017 at 10:07 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Can you send the part of your colvars input that defines the distance
> colvar?
>
> Jerome
>
> On 8 July 2017 at 18:08, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>
>> Hi Jerome:
>> That helps, thank you.
>>
>> My question stemmed from observing a major discrepancy for the distance
>> between the centers of mass of the protein and the ligand according to how
>> it is measured.
>>
>> With the same files from a "wrapAll no" MD simulation (just now
>> completed) loaded to vmd,
>>
>> set selprot [atomselect top "protein"]
>> measure center $selprot
>> set sellig [atomselect top "segname SAA1"]
>> measure center $sellig
>> set dist [ veclength [vecsub [measure center $selprot] [measure center
>> $sellig]]]
>>
>> gives 28A
>>
>> while cv printframe gives 8A, which is totally unrealistic, much too
>> small.
>>
>> This is just the same that I observed from MD simulations with "wrapAll
>> on".
>>
>> My first hypothesis was that "cv printframe", for reasons that I do not
>> understand, is taking into account the sole chain of the receptor where the
>> ligand resides (although even so a 8A is probably not enough. As "cv
>> printframe" is wrong about "r", perhaps it is also wrong about Theta, etc.
>>
>> I assume that I am doing something wrong and I am embarrassed in coming
>> again here with the same problem (however, I am now here with a MD "wrapAll
>> no", as required for measuring centers when there is more than one
>> molecule. I do not see any overlapping between the periodic boxes, and the
>> whole protein-ligand is within. There are two other ligands, one in each
>> chain, common ligands in biochemistry.
>>
>> Thanks for your (and all guys) understanding.
>>
>> francesco pietra
>>
>> On Sat, Jul 8, 2017 at 12:46 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
>> wrote:
>>
>>> Hi Francesco,
>>>
>>> That should not be a problem, as long that you make sure your
>>> multi-chain receptor always stays in one piece, and is never split across
>>> several periodic cells
>>>
>>> Jerome
>>>
>>> On 7 July 2017 at 17:21, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>>>
>>>> Hello:
>>>> Does anyone know whether ABF and FEP simulations can be carried out
>>>> with namd on a two-chains protein containing a ligand in one of the two
>>>> chains?
>>>> i am referring to, in particular, the 2017 tutorial protein-ligand.
>>>>
>>>> thanks
>>>>
>>>> francesco pietra
>>>>
>>>
>>>
>>
>

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