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Joined: Jan 2004
Posts: 60
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Joined: Jan 2004
Posts: 60
Dear all:
I got a problem of CHARMm on insight II.
I constructed a monolayer of 96 chains of HS(CH2)11CH3.
I needed to minimize them, and I set some constraints, such as harmonic all S atoms or all C atoms or all molecule.
From insightII, I knew my setting is OK. But, after minimization, I found they didn't be constrained. How do I use the harmonic constraint?
My input file is as follows:
* Script file produced by INSIGHT
*
! Startup script for CHARMm
!
UPPER ! case for file to write
BOMBLEVEL -2
WRNLEV 0
PRNLEV 5
! Script to read parameter, psf and crd file
!
OPEN READ UNIT 21 CARD NAME "top_all27_prot_na.rtf"
READ RTF UNIT 21 CARD
CLOSE UNIT 21
OPEN READ UNIT 21 CARD NAME "charmm27_support.rtf"
READ RTF UNIT 21 CARD APPEND
CLOSE UNIT 21

CLOSE UNIT 21
OPEN READ UNIT 21 CARD NAME "P2SAM4X4.rtf"
READ RTF UNIT 21 CARD APPEND
CLOSE UNIT 21

OPEN READ UNIT 20 CARD NAME "par_all27_prot_na.prm"
READ PARA UNIT 20 CARD
CLOSE UNIT 20

OPEN READ UNIT 20 CARD NAME "P2SAM8X4.psf"
READ PSF UNIT 20 CARD
CLOSE UNIT 20

OPEN READ UNIT 20 CARD NAME "p2sam8x4_8.crd"
READ COOR UNIT 20 CARD
CLOSE UNIT 20




CONStraint HARMonic SELE BYNUm 36 .OR. -
BYNUm 75 .OR. -
BYNUm 114 .OR. -
BYNUm 153 .OR. -
BYNUm 192 .OR. -
BYNUm 231 .OR. -
BYNUm 270 .OR. -
BYNUm 309 .OR. -
BYNUm 348 .OR. -
BYNUm 387 .OR. -
BYNUm 426 .OR. -
BYNUm 465 .OR. -
BYNUm 504 .OR. -
BYNUm 543 .OR. -
BYNUm 582 .OR. -
BYNUm 621 .OR. -
BYNUm 660 .OR. -
BYNUm 699 .OR. -
BYNUm 738 .OR. -
BYNUm 777 .OR. -
BYNUm 816 .OR. -
BYNUm 855 .OR. -
BYNUm 894 .OR. -
BYNUm 933 .OR. -
BYNUm 972 .OR. -
BYNUm 1011 .OR. -
BYNUm 1050 .OR. -
BYNUm 1089 .OR. -
BYNUm 1128 .OR. -
BYNUm 1167 .OR. -
BYNUm 1206 .OR. -
BYNUm 1245 END FORCE 300.000000

some of my output file is as follows,
CHARMM>

CHARMM> CONS HARM FORCE 200 MASS SELE atom * * END COMP

***** LEVEL 0 WARNING FROM *****
***** Unexpected end during parsing
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 0

CSTRAN: Harmonic Restraints
ABSOlute type as set number 1. Number of selected atoms: 0
Reference coordinates set to comparison coordinates.
Mass weighting will be used for new restraints.
The force constant of 200.00000 will be used.
An exponent of 2 will be used.
The XYZ scale factors are: 1.00000 1.00000 1.00000
A total of 0 atoms are restrained.

Joined: Sep 2003
Posts: 8,605
Likes: 23
rmv Online Content
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It's a little confusing, because your script and the output shown aren't exactly the same.

The biggest problems are with the atom selections; one is incorrect, the other may be correct but is somewhat cumbersome, both to write and to understand. The easy one first--

CHARMM> CONS HARM FORCE 200 MASS SELE atom * * END COMP
***** LEVEL 0 WARNING FROM *****
***** Unexpected end during parsing

The ATOM keyword requires 3 text identifiers, in the order SEGID, RESID, TYPE; the END keyword is being interpreted as the atom name (TYPE), and is therefore confuses the CHARMM command parser. A more correct form would be SELE atom * * * END and is the same as SELE ALL END (which is the default), and possibly not what is intended, and usually not needed.

The FORCE parameter seems overly large, when used in conjunction with the MASS keyword.

In the the case of the long list of BYNUM atom selections, it isn't clear if it is correct without examing the PSF or a CHARMM formatted coord file (.crd). I'd guess that some other computer program created the text for that command-- there are easier ways for humans to use. The following examples assume each thiol is a separate RESIdue in a segment named TH, and each is numbered S-C1-C2-C3- etc.

! RESTRAINT ON HEAVYATOMS ONLY
cons harm mass force 50. sele .not. type H* end
mini ...
! CLEAR RESTRAINTS
cons harm clear
! REDUCE FORCE, RESTRAIN JUST "S" END OF CHAIN
cons harm mass force 25. sele atom TH * S .or. atom TH * C1 -
.or. atom TH * C2 .or. atom TH * C3 end
mini ...
! CLEAR RESTRAINTS, FINAL MIN
cons harm clear
mini ...




Rick Venable
computational chemist


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