AMBER Archive (2008)

Subject: Re: AMBER: protonate in Amber10

From: David A. Case (case_at_scripps.edu)
Date: Thu May 29 2008 - 16:10:34 CDT

On Wed, May 28, 2008, Benjamin Juhl wrote:
>
> i wanted to use protonate on a pdb file, but the outputfile was always
> empty. That is if i used the protonate from amber10 - if i use protonate
> from amber9 everthing works fine.

I can't reproduce this, but I used g95 as the compiler (I don't have
patthscale). So I don't think it is something intrinsic to the code itself.

There is only one tiny change between Amber9 and Amber10 source codes:

diff -u -r9.0 -r10.0
--- protonate.f 3 Apr 2006 23:35:48 -0000 9.0
+++ protonate.f 15 Apr 2008 23:24:05 -0000 10.0
@@ -46,7 +46,7 @@
       character*4 camide, camidet(3)
       character*1 ctemp1
       logical first, header, aminot, nterm(MAXAT), ter(MAXAT)
- integer minres, maxres, ksave, lname,
+ integer minres, maxres, ksave, lname, ios,
      . iat, icout, ic, iar, nscat, i, j, k, l, m, n,
      . nrs, nhyd, lres
 c
@@ -71,7 +71,8 @@
    30 continue
       iat = 1
       do icout = 1, MAXAT
- read( nfilin, '(a80)', end=40 ) inline
+ read( nfilin, '(a80)', iostat=ios ) inline
+ if( ios>0 ) go to 40
         if ( inline(1:3) .eq. 'END' ) go to 40
 c
 c -- (following line assumes that the alternate conformation flag

Unless pathscale is not recognizing the "iostat=ios" construct, everything
should be the same. And it certainly doesn't explain why some pdb files work
and others fail (but work with Amber9).

I'm out of clues here.....dac

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