# Re: [AMBER] NMR restraint

From: Ming Tang <m21.tang.qut.edu.au>
Date: Thu, 21 Jul 2016 01:10:54 +0000

Thank you David,

I guess 2,3,4,5 are residue number in group 1 from igr2=1,1,1. But "COM1 is defined by # {C1 in residue 1; C1 in residue 2; N2 in residue 3; C1 in residue 4}" confused me. So, it is actually "COM1 is defined by # {C1 in residue 1; C1 in residue 2; N2 in residue 3; C1 in residue 4}" ?

-----Original Message-----
From: David A Case [mailto:david.case.rutgers.edu]
Sent: Thursday, 21 July 2016 7:32 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] NMR restraint

On Wed, Jul 20, 2016, Ming Tang wrote:
>
> I am confused on the following commands in 24.11.5 of amber 16 manual (P481)"
>
> # 1) Define two centers of mass. COM1 is defined by # {C1 in residue
> 1; C1 in residue 2; N2 in residue 3; C1 in residue 4}.
> # COM2 is defined by {C4 in residue 1; O4 in residue 1; N* in residue 1}.
> # (These definitions are effected by the igr1/igr2 and grnam1/grnam2 #
> variables; You can use up to 200 atoms to define a center-of-mass #
> group) # 2) Set up a distance restraint between COM1 and COM2 which
> goes from a # target value of 5.0A to 2.5A, with a force constant of
> 1.0, over steps 1-5000.
> #
> &rst iat=-1,-1, nstep1=1,nstep2=5000,
> iresid=1,irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
> r1=0.00000E+00,r2=5.0000,r3=5.0000, r4=99.000,rk2=1.0000,rk3=1.0000,
> r1a=0.00000E+00,r2a=2.5000,r3a=2.5000,
> r4a=99.000,rk2a=1.0000,rk3a=1.0000,
> igr1 = 2,3,4,5,0, grnam1(1)='C1',grnam1(2)='C1',grnam1(3)='N2',
> grnam1(4)='C1', igr2 = 1,1,1,0,
> grnam2(1)='C4',grnam2(2)='O4',grnam2(3)='N*',
> /
>
> what is 2,3,4,5,0 and what is i in grnam1(i)?

2,3,4,5 are the residue numbers for the four atoms involved in the COM group; "0" is a flag indicating the end of the list.

grnam1(i) for i=1,2,3,4 are the atom names of the four atoms involved in this group.

...hope this helps....dac

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Received on Wed Jul 20 2016 - 18:30:02 PDT
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