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
