Fwd: ABF FEP with multichain receptor

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Jul 10 2017 - 05:25:30 CDT

Perhaps I was wrong assuming that "r" should be the distance between the
centers of mass of the ligand and the protein.
---------- 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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