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#34443 - 10/02/14 02:11 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
rmv Online   content

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Registered: 09/17/03
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I'm guessing that there's a problem with the input and some clues about the problem in the output; without more information it's difficult to make any suggestions.
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Rick Venable
computational chemist


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#34444 - 10/02/14 02:20 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
Mih Offline
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Registered: 02/10/13
Posts: 25
Also, could you please tell me if these numbers:

calc mxa @NL * 6 * 4
calc mxs 10 + @NL*2 * 4
calc mxt 500 * @N

will have to change in my script?

What is the significance if 15 here:

if c gt 15 goto eskip
if ug eq 0 then

Thank you,
Mihaela

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#34445 - 10/02/14 02:21 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
Mih Offline
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Registered: 02/10/13
Posts: 25
Also, in the line:

define unsat sele atom D 1 C2@C .and. chem CEL1 end

what is the meaning of 1, chem and CEL1?
Thank you,
Mihaela

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#34446 - 10/02/14 03:48 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
rmv Online   content

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Registered: 09/17/03
Posts: 8392
Loc: 39 03 48 N, 77 06 54 W
calc mxa @NL * 6 * 4
calc mxs 10 + @NL*2 * 4
calc mxt 500 * @N


These lines compute the values needed for CORREL startup, i.e. MAXAtoms, MAXSeries, and MAXTimesteps; their meaning is described in correl.doc

The value '500' may need to be changed, as it is based on the number of stored coordinate sets in each trajectory file. The variable @NL is the number of lipid molecules, and is set near the top of the main script.


if c gt 15 goto eskip
if ug eq 0 then


The above two lines are exception code added specifically for POPC, where the gamma chain (a.k.a. chain 1) has only 16 C atoms.


define unsat sele atom D 1 C2@C .and. chem CEL1 end
what is the meaning of 1, chem and CEL1?

Another atom selection issue (select.doc); the CHEM token allows one to select atoms based on their parameter type, rather than a IUPAC style label. The CEL1 parameter type is specific for a C atom involved in a C=C double bond.
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Rick Venable
computational chemist


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#34447 - 10/02/14 05:40 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
Mih Offline
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Registered: 02/10/13
Posts: 25
When I run the program, I get no errors, but no atoms are selected:

CHARMM> ! unsaturation check; beta chain
CHARMM> set ub = 0
Parameter: UB <- "0"

CHARMM> define unsat sele atom A 1 C2@C .and. chem CEL1 end
Parameter: C -> "2"
SELRPN> 0 atoms have been selected out of 36716

What am I doing wrong?
Thank you,
Mihaela

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#34448 - 10/02/14 05:47 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
rmv Online   content

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Registered: 09/17/03
Posts: 8392
Loc: 39 03 48 N, 77 06 54 W
Nothing is wrong; that test only succeeds if chain position 2 has a double bond (chem CEL1). For POPC, only positions 9 and 10 of the beta chain (chain 2) have a double bond.
_________________________
Rick Venable
computational chemist


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#34449 - 10/02/14 06:04 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
Mih Offline
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Registered: 02/10/13
Posts: 25
Right, I get no errors in the output file, but the order parameter output is invariably 0, regardless what value I assign to C:

For example, for C=2, I get:

SR2 0 0
SS2 0 0
SX2 0 0
SY2 0 0

Where could the error be?

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#34450 - 10/02/14 06:19 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
rmv Online   content

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Registered: 09/17/03
Posts: 8392
Loc: 39 03 48 N, 77 06 54 W
There are probably messages in the output file which give some indication of the problem.
_________________________
Rick Venable
computational chemist


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#34453 - 10/02/14 07:19 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
Mih Offline
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Registered: 02/10/13
Posts: 25
I think the problem is in the trajectory (dcd file)for POPC. I had POPC in water, so I needed only the trajectory for POPC. Maybe my method of selecting only the lipids was wrong, because I got a mismatch in the number of atoms from psf file for lipids and the trajectory file for lipids.
Do you have a recommendation of how to obtain the trajectory file for POPC only from the trajectory file of POPC in water?

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#34455 - 10/02/14 08:57 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
rmv Online   content

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Registered: 09/17/03
Posts: 8392
Loc: 39 03 48 N, 77 06 54 W
I usually keep the water.
_________________________
Rick Venable
computational chemist


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