AMBER Archive (2009)

Subject: [AMBER] Question about distance restraint ?

From: xuemeiwang1103 (xuemeiwang1103_at_163.com)
Date: Fri Oct 23 2009 - 05:07:47 CDT

Hi:
 I have a acetate ion of which the O atom should form a weak hydrogen bond whith the H atom of tyr423 residue in my protein system .When I have done my MD simulation,the two separate .In order to solve this,I want to restraint the distance of the two within 3.0A.After read the manual and searched the same problems on the website,I have written the input file but it seems wrong .Could sameone kind enough tell me the reason?Thank you!
input fire:
Stage 1- minimisation of 1opd
&cntrl
 imin=1,maxcyc=10000,ncyc=2000,
 ntb=1,igb=0,ntr=1,
 cut=8.0,
 ntpr=100,
 nmropt=1,
&end
&wt type='REST',istep1=1,istep2=10000,
 value1=1.0,
 value2=1.0,&end
&wt type='END'/
 LISTOUT=RST.OUT
DISANG=dis.RST
 NMR DISTANTENT.FILE
 &rst iresid=0,iat=9292,7786,r1=1.5,r2=2.5,r3=3.0,r4=3.04,rk2=8000,rk3=8000,/
&end
By the way,I am not confident in my inputfile ,because many parameters such as r1,r2 value which are set randomly,also the rk.Besides I am also not sure whether all the things done like this .Thank you again!

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