From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jan 24 2007 - 08:07:40 CST
Hi Himanshu,
Could you be a little more specific as to how the different topology is
causing the problem? Was your topology not applied? Or did your membrane
end up being the wrong size?
If you're using your own box, you also need to make sure you have
segments named LIP1, LIP2, and TIP3, like those in the default POPC and
POPE boxes.
Peter
PS. While VMD-L is the appropriate forum for this discussion now, if you
need to cross-post please do so as one email to both lists, rather than
two emails to separate lists.
Himanshu Khandelia wrote:
> Hi,
>
> I realized that the problem was because my topology for the lipid was
> different than the once used by the membrane plugin.
>
> Can anyone please advise me how to alter the membrane.tcl script to use it
> from my own user-defined directory location ? I tried to make the
> following changes in the section of the script where I thought the
> directory locations were specified. But this did not work.
>
> ################
> # set package WD and files
> global env
> if ([info exists env(MEMBRANEDIR)]) {
> # set psffile $env(MEMBRANEDIR)/${lipid}_box.psf
> # set pdbfile $env(MEMBRANEDIR)/${lipid}_box.pdb
> # set topfile $env(MEMBRANEDIR)/top_all27_prot_lipid.inp
> set pdbfile ~/${lipid}_box.pdb
> set psffile ~/${lipid}_box.psf
> set topfile ~/top_all27_prot_lipid.inp
> } else {
> # set psffile [file normalize [file dirname [info script]]]/${lipid}_box.psf
> # set pdbfile [file normalize [file dirname [info script]]]/${lipid}_box.pdb
> # set topfile $env(MEMBRANEDIR)/top_all27_prot_lipid.inp
> set pdbfile ~/${lipid}_box.pdb
> set psffile ~/${lipid}_box.psf
> set topfile ~/top_all27_prot_lipid.inp
> }
> set tempfile temp
> ################
>
> P.S: I was not able to modify the topology file or the membrane.tcl script
> in its original location
> (/usr/local/lib/vmd/plugins/noarch/tcl/membrane1.0/) because of permission
> problems.
>
> Thank you very much for the help,
>
> -Himanshu
>
> (I have also copied this message to the VMD list as it might be useful for
> people in the future there)
>
> On Tue, 23 Jan 2007, Brian Bennion wrote:
>
>
>> Hello,
>> Can you post your pdf and psf files? It might be that the psf file as an
>> extra bond between to very distant atoms. Viewing the pdb file with VMD will
>> not find this kind of error. I assume that viewing the psf and pdb together
>> doesn't lead to any weirdness?
>>
>> Brian
>>
>> At 09:32 AM 1/23/2007, Himanshu Khandelia wrote:
>>
>>> Hi,
>>>
>>> I built a membrane using the membrane module and then solvated it using
>>> solvate. The final system therefore has a lot of overlaps in the lipids,
>>> and also has a thin (~ 1 A) vaccum slice between the water generated by
>>> solvate and the water obtained from using the membrane module. When I
>>> tried to minimize the system in NAMD, I got the bad global exclusion count
>>> error.
>>>
>>> The initial energy is obviously very high. As per earlier discussions on
>>> the list, I tried each of the following, but nothing worked:
>>>
>>> - increasing/decreasing periodic cell dimensions
>>> - increasing/decreasing cutoffs
>>> - with/without rattle
>>> - checked lipid and water parameters, all is ok
>>> - looked at the pdb in vmd, there are no extra-long bonds
>>>
>>> Can anyone suggest anything else that might work ? The config file is
>>> attached, and part of the output is below
>>>
>>> Thank you very much
>>>
>>>
>>> ###################
>>> Warning: Bad global exclusion count, possible error!
>>> Warning: Increasing cutoff during minimization may avoid this.
>>> ETITLE: TS BOND ANGLE DIHED
>>> IMPRP ELECT VDW BOUNDARY MISC
>>> KINETIC TOTAL
>>>
>>> ENERGY: 0 99999999.9999 99999999.9999 99999999.9999
>>> 60.0134 39664966.2394 99999999.9999 0.0000 0.0000
>>> 0.0000 99999999.9999
>>>
>>> OPENING EXTENDED SYSTEM TRAJECTORY FILE
>>> TCL: Minimizing for 2000 steps
>>> Warning: Bad global exclusion count, possible error!
>>> Warning: Increasing cutoff during minimization may avoid this.
>>> ETITLE: TS BOND ANGLE DIHED
>>> IMPRP ELECT VDW BOUNDARY MISC
>>> KINETIC TOTAL
>>>
>>> ENERGY: 0 99999999.9999 99999999.9999 99999999.9999
>>> 60.0134 39664966.2394 99999999.9999 0.0000 0.0000
>>> 0.0000 99999999.9999
>>>
>>> INITIAL STEP: 1e-06
>>> GRADIENT TOLERANCE: nan
>>> BRACKET: 0 nan nan nan nan
>>> RESTARTING CONJUGATE GRADIENT ALGORITHM
>>> ..
>>> ..
>>> ..
>>> ################################################
>>>
>>> ----------------------------
>>> Himanshu Khandelia
>>> Research Assistant Professor (Postdoc)
>>> MEMPHYS, Center for Membrane Physics
>>> University of Southern Denmark (SDU)
>>> Odense M 5230, Denmark
>>> www.memphys.sdu.dk
>>> Phone: +4565503510
>>> email: hkhandel_at_memphys.sdu.dk
>>> -----------------------------
>>>
>>>
>>>
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