Dear Amber,
I have a system with some atom centers that are simply put "way too
close" and I'm trying to optimize using geometry only in Sander.
Is there a way to turn off the nonbonded (vdw and elec) interactions and
only due geometry optimization in Sander?
Setting SCNB, SCEE and DIELC >> 1 takes care of electrostatics and the
1-4 vdw and electrostatic interactions,
but still leaves vdw interactions.
Setting CUT << 1.0 should take care of vdw but gets me into trouble b/c
the number of nbond interactions exceeds some array limits
and this is probably not a good idea for anything other than NTB=0 !!!
I'm sure there are other tricks I could play with parameters, but the
best solution is to simply turn off these energy functions,
and I haven't found a way to do this. NTT only lets me turn off the
bonded terms not the nonbonded terms :-(
Can you help?
NOTE: Geometry optimization is a cute trick to generate coordinates for
small molecules using only random initial
coords, if vdw and electrostatic interactions are turned off then atoms
can pass thru each other as necessary during optimization. Granted the
resulting structures are 1) not necc. global energy min. and 2) have
random chirality. Nonetheless I used this scheme w/ XPLOR to generate
structures for all 20a.a. starting with only topology files and it
worked ok.
In short it's a cute trick to place a limited number of missing atoms
when you have nothing to work with but the toplogy.
Thanks in advance.
TOm
--
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Thomas C. Bishop, Ph.D.
Joint Faculty Appointments Program Professor
Center for Bioenvironmental Research
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Tulane University Office
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Dept. of Environmental Health Sciences(SL-29)
School of Public Health & Trop. Medicine
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Phone: 504-988-6203 Fax: 504-585-6428
bishop_at_tulane.edu
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Xavier University Office
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Division of Basic Pharmaceutical Sciences
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Received on Mon Oct 07 2002 - 13:17:52 PDT
