From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jul 11 2017 - 11:28:48 CDT
Hi Jerome:
With a new definition of colvars, replacing the absurd one I had first
devised, ABF Conformation Bound runs OK. Thank you very much.
A side question: I am using "rigid bonds water" "ts=1.0fs". Is that safe
rigidifying all bonds, to speed up, with ts=2.0fs, in these ABF and FEP
simulations?
thanks
francesco
On Tue, Jul 11, 2017 at 3:12 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> 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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