AMBER Archive (2004)

Subject: Re: AMBER: MD with NTR + NMROPT

From: David A. Case (case_at_scripps.edu)
Date: Wed May 12 2004 - 14:09:24 CDT

On Wed, May 12, 2004, anshul_at_imtech.res.in wrote:
>
> After this I used the nmropt=1 and also kept the group information at the
> end but now it is not reading the group information and gives error. here
> is my new input
>
> &ewald
> eedmeth=5,
> &end
> &cntrl
> imin=0, cut=30, nstlim=30000, ntt=1, ntx=1, irest=0,
> ntpr=200, ntwx=500, ntwe=500, tempi=10,
> ntb=0, ntr=1, dielc=4, vlimit=30, nmropt=1,
> &end
> &wt type='TEMP0', istep1=0,istep2=15000,value1=10.0,
> value2=500.0, &end
> &wt type='TEMP0', istep1=15001,istep2=20000,value1=500.0,
> value2=500.0, &end
> &wt type='TEMP0', istep1=20001,istep2=25000,value1=500.0,
> value2=300.0, &end
> &wt type='TEMP0', istep1=25001,istep2=30000,value1=300.0,
> value2=300.0, &end
> &wt type='TAUTP', istep1=0,istep2=20000,value1=0.5,
> value2=0.2 &end
> &wt type='TAUTP', istep1=20001,istep2=25000,value1=2.0,
> value2=2.0 &end
> &wt type='TAUTP', istep1=25001,istep2=30000,value1=0.5,
> value2=0.2 &end
> &wt type='END' &end
> Input for restrained residues (A1-A166)
> 2
> RES 1 167
> END
> Input for restrained residues (A182-A276)
> 2
> RES 182 276
> END
> END
>
> this is the part of the output file with the error
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> &ewald
> GROUP 1 HAS HARMONIC CONSTRAINTS 46.00000
> GRP 1 RES 296 TO 288
> GRP 1 RES 6 TO 6
> ***PROBLEMS WITH GROUPimin 296***** 6 6 -4 0 0 0 0
> 0 0 0 0 0*******
> GRP 1 RES 4996 TO 288
> GRP 1 RES 96 TO 96 GRP 1 RES 6 TO 36
> GRP 1 RES 296 TO 6
> ***PROBLEMS WITH GROUP&wt -94***** 0 0 0 0 0 0 0
> 0 0 0 0 0*******
> rfree: Error decoding variable 2 2 from:
> value2=500.0, &end

You should place the &ewald namelist after the &cntrl namelist, not before it.
Obviously, you want the title of group 1 to be "Input for restrained residues
(A1-A166)" and not " &ewald". You may also need a blank line after the final
"&wt" card (for the empty section THREE input (although I think that is not
necessary).

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu