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#24587 06/16/10 02:32 PM
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Edo Offline OP
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Hi All,
I wasn't sure whether to post this here, or the Parameter Set section. Anyway, I have the following problem. I am using wild card characters in the NBFIX section of my parameter file:

NBFIX
S* A* -0.2 5.0

When I run a simulation I get the following warning from CHARMM:

***** LEVEL -1 WARNING FROM <PARRDR> *****
***** NBFIX involves an atom in a vdw group; Whole VDW group modified
******************************************

My question is, does this warning mean my simulation will not run properly? Despite this warning message, it seems as though the parameters are defined correctly internally in CHARMM because when I issue a 'print param' in the script the parameters seemed to have been modified correctly. For example here are four LJ parameters that seem to have been correctly modified:

9184 A57 ---SG 48828125.00 6250.00 5.000 -0.2000 48828125.00 6250.00 5.000 -0.2000 0
9185 A57 ---SA 48828125.00 6250.00 5.000 -0.2000 48828125.00 6250.00 5.000 -0.2000 0
9186 A57 ---SV 48828125.00 6250.00 5.000 -0.2000 48828125.00 6250.00 5.000 -0.2000 0
9187 A57 ---SL 48828125.00 6250.00 5.000 -0.2000 48828125.00 6250.00 5.000 -0.2000 0

Here are sample residues from my topology file containing example A* and S* residues (note that I do not use 'group' labels in the residue definitions - perhaps this is the cause of the warning?):

RESI G2 0.0
GROUP
Atom A A2 0.0
Bond A +A
Angle -A A +A
DIHE -A A +A #A

RESI SW 0.0
GROUP
ATOM SW SW 0.0
PATCHING FIRST NONE LAST NONE

See any fatal flaws with running a simulation with the above warning? Visually the simulations seem to run fine, but wanted to make sure I'm not missing something.
Thanks!
Ed

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rmv Online Content
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I believe it's a warning related to the wildcard usage, a way to make sure that you really wanted to change ALL interactions between the two "groups" indicated by the wildcards. It's somewhat outside expected usage, hence the warning.


Rick Venable
computational chemist

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Edo Offline OP
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much appreciated, thanks Rick.


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