VMD-L Mailing List

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Wed Dec 09 2009 - 13:01:58 CST

Hi, Francesco:

I just downloaded a fresh VMD 1.8.7 from http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
  , and checked the rbcg-2007.top file. It gives me the following
entry :
RESI POPC 0.00
GROUP
ATOM CHO Qo 0.70 ! Choline head group
ATOM PHO Qa -0.70 ! Phosphate
ATOM ES1 Na 0.00 ! Ester group
ATOM ES2 Na 0.00 ! Ester group
ATOM ME1 C 0.00 ! lipid tail
ATOM ME2 C 0.00 ! lipid tail
ATOM ME3 CDB 0.00 ! lipid tail double bond
ATOM ME4 C 0.00 ! lipid tail
ATOM MT1 C 0.00 ! lipid tail terminus
ATOM ME5 C 0.00 ! lipid tail
ATOM ME6 C 0.00 ! lipid tail
ATOM ME7 C 0.00 ! lipid tail
ATOM MT2 C 0.00 ! lipid tail terminus
BOND CHO PHO PHO ES1 ES1 ES2 ES1 ME1
BOND ME1 ME2 ME2 ME3 ME3 ME4 ME4 MT1
BOND ES2 ME5 ME5 ME6 ME6 ME7 ME7 MT2

I think the one you are using is supposed to be DOPC, and they differ
by a double bond, which is highlighted as red.

Best,
Bin

On Dec 9, 2009, at 10:49 AM, Francesco Pietra wrote:

> Hello Bin:
> I have been looking for woodcocks with my brittany this morning,
> therefore I may be momentarily out of the rules of chemsitry and I do
> not understand your point. I can compare Anton's post with my own:
>
> Anton:
>
> RESI POPC 0.00
> GROUP
> ATOM CHO Qo 0.70 ! Choline head group
> ATOM PHO Qa -0.70 ! Phosphate
> ATOM ES1 Na 0.00 ! Ester group
> ATOM ES2 Na 0.00 ! Ester group
> ATOM ME1 C 0.00 ! lipid tail
> ATOM ME2 C 0.00 ! lipid tail
> ATOM ME3 C 0.00 ! lipid tail
> ATOM MT1 C 0.00 ! lipid tail terminus
> ATOM ME4 C 0.00 ! lipid tail
> ATOM ME5 C 0.00 ! lipid tail
> ATOM ME6 C 0.00 ! lipid tail
> ATOM MT2 C 0.00 ! lipid tail terminus
> BOND CHO PHO PHO ES1 ES1 ES2 ES1 ME1
> BOND ME1 ME2 ME2 ME3 ME3 MT1 ES2 ME4
> BOND ME4 ME5 ME5 ME6 ME6 MT2
>
>
> Me (the same I posted previously):
>
> ATOM 2463 CHO POPCO 1 37.490 25.415 4.653 1.00
> 0.00 O1 C
> ATOM 2464 PHO POPCO 1 39.740 24.614 0.940 1.00
> 0.00 O1 P
> ATOM 2465 ES1 POPCO 1 37.568 20.460 -0.263 1.00
> 0.00 O1
> ATOM 2466 ES2 POPCO 1 37.020 21.866 -4.322 1.00
> 0.00 O1
> ATOM 2467 ME1 POPCO 1 36.057 16.858 1.933 1.00
> 0.00 O1
> ATOM 2468 ME2 POPCO 1 35.653 13.060 0.274 1.00
> 0.00 O1
> ATOM 2469 ME3 POPCO 1 37.948 9.854 -0.816 1.00
> 0.00 O1
> ATOM 2470 MT1 POPCO 1 38.047 4.914 0.293 1.00
> 0.00 O1
> ATOM 2471 ME4 POPCO 1 35.557 18.929 -6.037 1.00
> 0.00 O1
> ATOM 2472 ME5 POPCO 1 36.308 15.668 -9.314 1.00
> 0.00 O1
> ATOM 2473 ME6 POPCO 1 37.484 11.986 -12.138 1.00
> 0.00 O1
> ATOM 2474 MT2 POPCO 1 37.279 8.543 -12.520 1.00
> 0.00 O1
> END
>
> and I see 12 beads in each, defining the oleoyl, palmitoyl and
> glyc+polar.head sections Could you please explain which particular
> bead is lacking in my definition of POPC? (for POPC I mean palmitoyl
> oleoyl phosphatidylcholine, forgetting here about sn stereochemistry)
>
> francesco
>
> On Wed, Dec 9, 2009 at 7:07 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
>> Dear Francesco:
>>
>> From the pdb segment you posted, it seems there is one bead missing
>> in the
>> definition of POPC lipid. Indeed, if you compare the rbcg-2007.top
>> file
>> posted at : http://www.ks.uiuc.edu/Research/CG/rbcg/files/ , with
>> the one
>> come with VMD 1.8.7, you will find the difference.
>>
>> Best,
>> Bin
>>
>>
>> On Dec 8, 2009, at 11:23 AM, Francesco Pietra wrote:
>>
>>> Hi:
>>> Do restraints on CG models apply like for all-atoms? For example, in
>>> order to restrain the polar head of POPC lipid
>>>
>>> ATOM 2463 CHO POPCO 1 37.490 25.415 4.653 1.00
>>> 0.00 O1
>>> C
>>> ATOM 2464 PHO POPCO 1 39.740 24.614 0.940 1.00
>>> 0.00 O1
>>> P
>>> ATOM 2465 ES1 POPCO 1 37.568 20.460 -0.263 1.00
>>> 0.00 O1
>>> ATOM 2466 ES2 POPCO 1 37.020 21.866 -4.322 1.00
>>> 0.00 O1
>>> ATOM 2467 ME1 POPCO 1 36.057 16.858 1.933 1.00
>>> 0.00 O1
>>> ATOM 2468 ME2 POPCO 1 35.653 13.060 0.274 1.00
>>> 0.00 O1
>>> ATOM 2469 ME3 POPCO 1 37.948 9.854 -0.816 1.00
>>> 0.00 O1
>>> ATOM 2470 MT1 POPCO 1 38.047 4.914 0.293 1.00
>>> 0.00 O1
>>> ATOM 2471 ME4 POPCO 1 35.557 18.929 -6.037 1.00
>>> 0.00 O1
>>> ATOM 2472 ME5 POPCO 1 36.308 15.668 -9.314 1.00
>>> 0.00 O1
>>> ATOM 2473 ME6 POPCO 1 37.484 11.986 -12.138 1.00
>>> 0.00 O1
>>> ATOM 2474 MT2 POPCO 1 37.279 8.543 -12.520 1.00
>>> 0.00 O1
>>> END
>>>
>>> are restraints to be applied to beads CHO and PHO? If so, by making
>>> the .fix file in VMD as if it were an all-atoms model are the
>>> restraint forces applied correctly?
>>>
>>> And if I want to restraint the whole protein and the whole bilayer
>>> (to
>>> work at constant pressure on the solvent water around), is any way
>>> to
>>> simply specify the range of residue numbers?
>>>
>>> That is, I assume to have to prepare the system for production as
>>> carefully as if it were all-atoms.
>>>
>>> thanks
>>> francesco pietra
>>
>>