AMBER Archive (2003)

Subject: Re: AMBER: nmanal's error message

From: David Case (case_at_scripps.edu)
Date: Mon Aug 18 2003 - 18:24:11 CDT

On Mon, Aug 18, 2003, Qiang Lu wrote:
>
> I used new2oldparm to convert parm7 to parm6, then ran nmanal.
>

Try the following patch to amber7/src/nmode/rdparm2.f:

*** rdparm2.f 25 Jul 2001 23:51:39 -0000 7.2
--- rdparm2.f 18 Aug 2003 23:16:49 -0000
***************
*** 27,33 ****
          READ(20,9108) (IHEAD1(I),I=1,20)
          READ(20,9118) NATOM,NTYPES,NBONH,MBONA,NTHETH,MTHETA,NPHIH,
       + MPHIA,NHPARM,NPARM,NNB,NRES,NBONA,NTHETA,NPHIA,
! + NUMBND,NUMANG,NPTRA,NATYP,NPHB
  C
  C ----- CHECK FOR POSSIBLE OVERFLOWS OF ARRAY BOUNDS -----
  C
--- 27,34 ----
          READ(20,9108) (IHEAD1(I),I=1,20)
          READ(20,9118) NATOM,NTYPES,NBONH,MBONA,NTHETH,MTHETA,NPHIH,
       + MPHIA,NHPARM,NPARM,NNB,NRES,NBONA,NTHETA,NPHIA,
! + NUMBND,NUMANG,NPTRA,NATYP,NPHB,ifpert,idum,idum,
! + idum,idum,idum,idum,idum,idum,idum,idum
  C
  C ----- CHECK FOR POSSIBLE OVERFLOWS OF ARRAY BOUNDS -----
  C

Let me know this helps. [Note: if you have the amber6 version of nmanal,
that should also work. In amber6 there was a test to see if one had the
Amber 2 (!!) or Amber 3 and later prmtop files. This test got lost in the
conversion to Amber 7, resulting in code that was looking for Amber 2 (ca.
1985) formatted files....]

...thanks for pointing this out....dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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