> 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?
>
I did that on the vdw part before. All I did was to edit prmtop manually.
Write a script and replace parameters of CN1 and CN2 by zeros. It should
take care of the vdw part.
> 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
>
>
>
>
>
> --
> -----------------------------------------
> Thomas C. Bishop, Ph.D.
> Joint Faculty Appointments Program Professor
> Center for Bioenvironmental Research
> -----------------------------------------
> Tulane University Office
> -----------------------------------------
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> Phone: 504-988-6203 Fax: 504-585-6428
> bishop_at_tulane.edu
> -----------------------------------------
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> -----------------------------------------
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> tbishop_at_xula.edu
> -----------------------------------------
>
>
Received on Mon Oct 07 2002 - 15:26:01 PDT
