# Re: AMBER: Distance Restraints

From: Esther Brugger <esther_brugger.yahoo.com>
Date: Wed, 3 Jan 2007 14:04:03 -0800 (PST)

Dear ALL,

In my previous email, I wrote the distance restraints (only a small part of this file) in the followings:

# Leu-NH & Hb
&rst iat=-1,-1, iresid=1,
r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
igr1 =1,2,3,4,5, grnam1(1) = 'H118',
igr2 =1,1,2,2,3,3,4,4,5,5, grnam2(1)= 'H140', grnam2(2)='H141',
/

But actually, I want to restraint the distance between H118 and H140, H141 in residue 1, residue 2, residue3...residue5 respectively. Do you think I should seperate these distance by following commands? Are they correct?

&rst iat=-1,-1, iresid=1,
r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
igr1 =1, grnam1(1) = 'H118',
igr2 =1,1, grnam2(1)= 'H140', grnam2(2)='H141',
/
&rst iat=-1,-1, iresid=1,
r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
igr1 =2, grnam1(1) = 'H118',
igr2 =2,2, grnam2(1)= 'H140', grnam2(2)='H141',
/
&rst iat=-1,-1, iresid=1,
r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
igr1 =3, grnam1(1) = 'H118',
igr2 =3,3, grnam2(1)= 'H140', grnam2(2)='H141',
/
&rst iat=-1,-1, iresid=1,
r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
igr1 =4, grnam1(1) = 'H118',
igr2 =4,4, grnam2(1)= 'H140', grnam2(2)='H141',
/
&rst iat=-1,-1, iresid=1,
r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
igr1 =5, grnam1(1) = 'H118',
igr2 =5,5, grnam2(1)= 'H140', grnam2(2)='H141',
/

Thank you very much for your advice!
Cheers

Esther Brugger <esther_brugger.yahoo.com> wrote: Dear Amber Users,

Now I am trying to put the "Leu-NH & Hb" distance restraints in the MD calcuations. Hb includes 2 H atoms. Here is the atoms that I want to add the restraints:
resid 1-5: H118 with resid 1-5: H140, H141 2.00 5.00
resid 1-5: H79 wtih resid 1-5: H101, H102 2.00 5.00
resid 1-5: H40 with resid 1-5: H62, H63 2.00 5.00
resid 1-5: H with resid 1-5: H22, H23 2.00 5.00
I need to specify the restraints between H118 and H140, H141 intra-residue, then average these 5 residues results.

Here is the DISANG file:
# Leu-NH & Hb
&rst iat=-1,-1, iresid=1,
r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
igr1 =1,2,3,4,5, grnam1(1) = 'H118',
igr2 =1,1,2,2,3,3,4,4,5,5, grnam2(1)= 'H140', grnam2(2)='H141',
/
&rst iat=-1,-1, iresid=1,
r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
igr1 =1,2,3,4,5, grnam1(1) = 'H79',
igr2 =1,1,2,2,3,3,4,4,5,5, grnam2(1)= 'H101', grnam2(2)='H102',
/
&rst iat=-1,-1, iresid=1,
r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
igr1 =1,2,3,4,5, grnam1(1) = 'H40',
igr2 =1,1,2,2,3,3,4,4,5,5, grnam2(1)= 'H62', grnam2(2)='H63',
/
&rst iat=-1,-1, iresid=1,
r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
igr1 =1,2,3,4,5, grnam1(1) = 'H',
igr2 =1,1,2,2,3,3,4,4,5,5, grnam2(1)= 'H22', grnam2(2)='H23',
/

Do you think it is correct to realize what I want for the restraints? Thanks a lot for your any suggestion and help!

All the bests,

Esther B.
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Received on Sun Jan 07 2007 - 06:07:14 PST
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