AMBER Archive (2009)

Subject: Re: [AMBER] Question about distance restraint ?

From: Carlos Simmerling (
Date: Fri Oct 23 2009 - 05:56:24 CDT

it's always important to look at the sander output and see what it says when
it reads your input.
does it recognize this restraint? what does the simulations do? do you get
an error message, or does it not do what you want? this information makes it
easier for us to help you.

a few comments:
the rk are too large. this is 8000 kcal/mol-A^2 try something like 10. you
can always put the rk into the equation for the harmonic restraint and see
how much variation you expect with thermal energy of RT
the r4 is too small, it needs to be at least a few A larger than r3. this is
where the potential becomes linear, so if you do it too close to the minimum
then the potential will be very flat.

2009/10/23 xuemeiwang1103 <>

> 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'/
> &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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