AMBER Archive (2009)

Subject: [AMBER] ERROR In Restraint file.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue Apr 28 2009 - 10:27:18 CDT

Dear Sir/Madam,

 

Sorry that I miss out some of the important information. The CASE1 files were using probably in single processor workstation, but when I copy the input files to supercomputer (just compiled with amber 8) and run using the following command line "mpirun /share1/amber8/exe/sander -O -i 3_md4.in -o 3_md7.out -c 3_md6.restrt -p xxx.prmtop -r 3_md7.restrt -x 3_md7.mdcrd &" The error message listed below as found.

 

I have also double checked the identify of atom p of residue 4 and atom n1 and n2 of residue 5. They are correct. I converted the xxx.prmtop and xxx.inpcrd file to pdb file. Then the pdb file was opened with DS visualizer. The residue numbers and atom names are same as those that I specified in the rst file.

 

Did I miss any important point here? What's wrong with the file? Please kindly help.

 

Best regards,

 

 

 

 

 
> From: askamber23_at_hotmail.com
> To: amber_at_ambermd.org
> Date: Tue, 28 Apr 2009 23:12:34 +0800
> Subject: [AMBER] ERROR In Restraint file.
>
>
>
> Dear Sir/Madam,
>
>
>
> I found the following error message when I do the umbrella samples using the following rst and in files. I was planning to do the restraint between atom P of residue 4 and the center of atom n1 and atom n2 of residue 5. Here is the results that I found when different rst files was used. Could you mind to instruct me what should I do to make the corrections?
>
>
> ===========================CASE 1========================
> &rst iat=4,5, r1=0.0, r2=3.0, r3=3.0, r4=100.0, rk2 =1.0, rk3 = 1., iresid=1,
> atnam(1) = p,
> atnam(2) = n1, atnam(2) = n2 /
>
> ERROR MESSAGE APPEARS ON THE TELNET SCREEN:
> >>PGFIO-F-239/namelist read/unit=33/entity name is not member of group.
> File name = 3.rst formatted, sequential access record = 2
> In source file _restal.f, at line number 302
>
> ===========================CASE 2========================
> &rst iat=4,5, r1=0.0, r2=3.0, r3=3.0, r4=100.0, rk2 =1.0, rk3 = 1., iresid=1,
> atnam(1) = 'p',
> atnam(2) = 'n1', atnam(2) = 'n2' /
>
>
> ERROR MESSAGE: CANNOT FIND ATOM P FOR RESIDUE 4, CANNOT FIND ATOM N10 AND N12 FOR RESIDUE 5. ERROR MESSSAGE AS FOLLOW LOCATED AT THE END OF THE LOG FILE
> --------------------------------------------------------------------
> RESTRAINTS:
> Requested file redirections:
> DISANG = 3.rst
> DUMPAVE = 3.result_md7
> Restraints will be read from file: 3.rst
> Here are comments from the DISANG input file:
>
> Error: No atom p in residue 4
> Error: No atom n2 in residue 5
> -----------------------------------------------------------------
>
> ===========================CASE 3========================
>
> &rst iat=4,5, r1=0.0, r2=3.0, r3=3.0, r4=100.0, rk2 =1.0, rk3 = 1., iresid=0,
> atnam(1) = 'p',
> atnam(2) = 'n1', atnam(2) = 'n2' /
>
> JOB CAN BE FINISHED, BUT THE DISTANCE OF ATOM4 AND ATOM5 WAS RESTRAINTED.
>
>
> ====================Input file=====================
> Production MD
> &cntrl
> imin = 0, irest = 1, ntx = 7, nmropt=1
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 100000, dt = 0.002,
> ntpr = 100, ntwx = 100, ntwr = 1000
> /
> &wt type='DUMPFREQ', istep1=10 /
> &wt type='END' /
> DISANG=3.rst
> DUMPAVE=3.result_md7
> END
> ==============================================
>
>
> Thank you very much!
>
>
>
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