AMBER Archive (2008)

Subject: Re: AMBER: aromatic residues lost planarity during MD simulation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Apr 21 2008 - 15:25:19 CDT

check the archives- this comes up often, and there was some discussion
earlier in 2008. look for nonplanar aromatic or similar in the web page
archive search tool.

On Mon, Apr 21, 2008 at 4:18 PM, <cniu_at_ualberta.ca> wrote:

> Dear all,
> I am running an md simulation using Amber9. After energy minimization and
> restrained dynamics (increasing the system temperature from Ok to 300K), I
> performed equilibration for 200ps and I found all the aromatic rings (in
> Phe, Tyr, His, etc) have lost their planarity. That sounds unreasonable but
> I cannot figure out what's wrong with my input file. I used leaprc.ff99 and
> my md input file follows,
>
> &cntrl
> imin = 0,
> ntx = 7, irest = 1,
> ntb = 2, pres0 =1.0, ntp = 1,
> taup = 2,
> ntr = 0,
> cut = 10,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 100000, dt = 0.002,
> ntpr = 100, ntwx = 500, ntwr = 1000
> /
> END
>
> Thanks in advance to anyone that will give any suggestion.
>
> Amara
>
>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
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Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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