AMBER Archive (2008)

Subject: Re: AMBER: protonate in Amber10

From: David A. Case (
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
@@ -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 -- (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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)