From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Jul 11 2017 - 08:12:51 CDT
Hi Francesco,
I thought your messages were self-explanatory. This looks like a mistake in
the colvar definition.
I don't think you need to enable forceNoPBC, by the way.
Jerome
On 11 July 2017 at 08:20, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> 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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