VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Dec 09 2009 - 12:49:28 CST

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
>
>