From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Jun 01 2012 - 03:15:21 CDT
Hello:
I remember rather vaguely that there are fixes to NAMD about dummy
atoms (which are otherwise taken as H-atoms bonded to one another).
As I am going to run amber parm7 with namd, while parameterizing
Ca(II) ions with "in" file:
0 0 2
------calcium--------------
Ca2
Ca2 INT 0
CHANGE OMIT DU BEG
0.0
1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.000
2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000
3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000
4 Ca C0 M 29.683 127.561 -18.450 2.00
DONE
STOP
and "dat" file:
Ca2+ vdw parameters from Concanavalin A study
MASS
C0 40.08 0.00
NONB
C0 1.7900 0.0140
I would be grateful for suggestions where such NAMD fixes can be found.
I am trying to use amber ff to compare the same system already worked
out with charmm 27 in NAMD. To this regard, how valuable the
parameterization of Ca(II) in charmm 27 is? Amber people warn that
currently fixed-charge amber parm7 parameters for divalent metal ion
are only to be used to neutralize charges, not pretending to
investigate interactions.
Thanks for advice
francesco pietra
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