Re: AMBER: Reg restraint value obtained during umbrella sampling

From: David A. Case <>
Date: Fri, 1 Jun 2007 18:19:35 -0700

On Fri, Jun 01, 2007, D.Usharani wrote:
> I realised the mistakes in the input file. so i tried doing the centre
> of mass distance restraint for two alanine residues seperated by 20
> angstroms and the input for restraint is
> &rst
> iat= -1,-1, nstep1=1, nstep2=5000,
> iresid=1,irstyp=0,ifvari=0,ninc=0,imulti=0,ir6=0,ifntyp=0,
> r1=0.00000, r2=20.0000, r3=20.0000, r4=99.0000,
> rk2=1.0000, rk3=1.0000,
> igr1 = 1,0,
> grnam1 (1) ='CA',
> igr2 = 2,0,
> grnam2 (1) ='CA',
> /

> I defined the ifvari =0 but still it didnt gave any restraint value in
> the out put file. It reads the restraint but not the r1,r2,r3,r4 and rk2
> and rk3 values.

This might be a bug: at least try out setting iresid=0 (which is the simplest
and most common case). Also, really be simple, and set iat>0: we need to find
something that works, then morph slowly into the things that fail.

It also might be caused by something external to the syntax above. Can you
post the entire input file?

Also, please post what version of Amber compiler, OS and architecture you are
using. (I apologize if you have given this earlier).

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Received on Sun Jun 03 2007 - 06:07:43 PDT
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