AMBER Archive (2009)

Subject: [AMBER] ERROR In Restraint file.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue Apr 28 2009 - 10:12:34 CDT

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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