AMBER Archive (2008)

Subject: Re: AMBER: sleap - TER-card

From: In Hee Park (ipark_at_chemistry.ohio-state.edu)
Date: Thu Jun 26 2008 - 19:31:40 CDT

That patch doesn't help for ambpdb to work it out. I am posting
prmtop/inpcrd (xxx.prmtop/xxx.inpcrd) files for the solvated ligand.
The pdb structure produced by "savepdb" is also posted (xxx.pdb).

$ ambpdb -p xxx.prmtop < xxx.inpcrd > check.pdb
| New format PARM file being parsed.
| Version = 1.000 Date = 05/22/06 Time = 12:10:21
At line 349 of file _ambpdb.f
Fortran runtime error: Bad value during integer read

Thanks for your help.
_____________
In-Hee Park

[2008-06-25.Wed.3:05pm] David A. Case wrote `Re: AMBER: sleap - TER-card'

  On Wed, Jun 25, 2008, In Hee Park wrote:
>
>
> $ ambpdb -p prmtop < inpcrd > pdb
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/22/06 Time = 12:10:21
> At line 349 of file _ambpdb.f
> Fortran runtime error: Bad value during integer read

  Can you check to see if the prmtop file has a "RADII" section? It looks like
  ambpdb is getting confused because the lack of a radii section is causing it
  to think this is an oldstyle prmtop file, but it's not. Or, maybe there is
  something else that is leading to this confusion.

  Anyway, please try the following patch to amber10/src/etc/ambpdb.f:

  --- ambpdb.f 16 Mar 2008 20:58:47 -0000 9.4
  +++ ambpdb.f 25 Jun 2008 20:44:57 -0000
  @@ -227,7 +227,7 @@
         SUBROUTINE GETNAM(NATOM,NRES,IGRAPH,IPRES,LBRES,ITITL,NF,KPF,
        1 X,IX,IH,ib,jb,nbond,chg,radius,lastat,ter,hasradii)
         character(len=4) igraph,lbres,ititl
  - logical ter,hasradii
  + logical ter,hasradii,oldstyle
         DIMENSION IGRAPH(*),IPRES(*),LBRES(*),ITITL(20)
         DIMENSION X(*),IX(*),IH(*),ib(*),jb(*),chg(*),lastat(*),radius(*)
         CHARACTER*80 FMT
  @@ -236,6 +236,7 @@
         AFMT = '(20A4)'
         RFMT = '(5E16.8)'
         hasradii = .false.
  + oldstyle = .false.
   C
   C ----- READ THE MOLECULAR TOPOLOGY -----
   C
  @@ -243,6 +244,7 @@
         TYPE = 'TITLE'
         CALL NXTSEC(NF, 0, 0,FMTIN, TYPE, FMT, IOK)
         READ(NF,FMT) (ITITL(I),I=1,20)
  + if( iok.eq.-1 ) oldstyle = .true.
   c
         FMTIN = IFMT
         TYPE = 'POINTERS'
  @@ -269,7 +271,7 @@
           chg(i) = chg(i)/18.2223
         end do
   c
  - if( iok.eq.-1 ) then ! this is an old-style prmtop file
  + if( oldstyle ) then
   c
           READ(NF,40) (X(I),I = 1,NATOM)
           READ(NF,30) (IX(I),I = 1,NATOM)
  @@ -341,7 +343,7 @@
   c --- prmtop file will have information needed to generate where the
   c TER cards in the output should be:
   c
  - if( iok.eq.-1 ) then ! old-style prmtop:
  + if( oldstyle ) then
             read(NF,30) (idummy,jdummy,kdummy,ldummy,i=1,ntheth)
             read(NF,30) (idummy,jdummy,kdummy,ldummy,i=1,ntheta)
             read(NF,30) (idummy,jdummy,kdummy,ldummy,mdummy,i=1,nphih)

  If this doesn't work (or even if it does) please consider posting the prmtop
  and inpcrd files that you gave to ambpdb: we need to track down the real
  origin of this problem.

  ...dac

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