Hi,
On Mon, September 27, 2010 10:01 pm, qiaoyan wrote:
> Dear amber users:
> I want to use ibelly to fix part of the protein, but is seems don't
> work properly, I can't identify what is the problem, anyone can help
when you did the simulation, what happend and what did you expect to
happen? Any output, error messages etc.? To say 'it did not work properly'
does not give us any information to help you.
Kind Regards,
Thomas
> me? Here is my input file:
>
> # Control section
> &cntrl
> nmropt=1,ipnlty=1,
> nstlim=50000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=500,ntwx=500,
> tempi=298.15, temp0=298.15, ntt=1, tautp=2.0,
> ntb=2, ntp=1,
> ntc=2, ntf=2,
> nrespa=1,
> cut = 10.0,
> ibelly=1,
> &end
> &ewald
> &end
> &wt type='REST',istep1=1,istep2=50000,
> value1=1.0, value2=1.0,&end
> &wt type='END', &end
> LISTOUT=dmd1.fout
> LISTIN=POUT
> DISANG=RST1.dist
> GROUP INPUT FOR IBELLY
> RES 1 24
> END
> GROUP INPUT FOR IBELLY
> RES 26 158
> END
> GROUP INPUT FOR IBELLY
> RES 160 174
> END
> GROUP INPUT FOR IBELLY
> RES 176 212
> END
> GROUP INPUT FOR IBELLY
> RES 214 6366
> END
> GROUP INPUT FOR IBELLY
> ATOM 363 366
> END
> GROUP INPUT FOR IBELLY
> ATOM 371 372
> END
> GROUP INPUT FOR IBELLY
> ATOM 2433 2436
> END
> GROUP INPUT FOR IBELLY
> ATOM 2449 2450
> END
> GROUP INPUT FOR IBELLY
> ATOM 2676 2679
> END
> GROUP INPUT FOR IBELLY
> ATOM 2688 2689
> END
> END
>
>
>
> 2010-09-28
>
>
>
> qiaoyan
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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Sep 27 2010 - 21:30:04 PDT
