Re: AMBER ff99SB on NAMD

From: Luca (bellucci14_at_unisi.it)
Date: Sun Nov 02 2008 - 02:26:52 CST

Hi Luis ,
it can depend on
rigidTolerance value. It is used for SHAKE-H convergence
and a value 5.0E-4 can not be appropriate.
You can check this with 1.0E-05 or better 1.0E-06 with 1-4scaling 0.83333
Point out that default value is 1.0E-08 for rigidTolerance.
Can you send your input file?
 Luca

> hi,
> I'm doing a simulation on NAMD using the ff99SB AMBER force field. According to NAMD instructions to use the AMBER ff with NAMD (http://www.ks.uiuc.edu/Research/namd/2.6/ug/node15.html) the following NAMD parameters:
>
> rigidTolerance 0.0001
> 1-4scaling 1.0
>
> should be changed to AMBER compatible values:
>
> rigidTolerance 0.0005
> 1-4scaling 0.83333
>
>
> However, while simulations with the first set maintain the protein conformation, simulations with the second set (recommended when using amber ff) destroy a few helices(not all!; the helix residues break apart into a random coil).
>
> Has anyone experienced this problem? What am I doing wrong?
>
>
>
>
> Thank you in advance for your help,
>
> Luis Cunha, PhD
> Dept. of Human Genetics
> Mount Sinai School of Medicine of the New York University
>
>
>

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