[AMBER-Developers] ambpdb -aatm prints nulls in output PDB

From: Tom Joseph <ttjoseph.gmail.com>
Date: Fri, 12 Feb 2010 18:08:28 -0500

The output of ambpdb -aatm contains null characters that can confuse
leap and other tools. This is because the "element" variable in
ambpdb.f90 is never set when -aatm is specified but it is printed
anyway. The patch below fixes the problem by not printing the element
field when -aatm is specified.

Thanks,
--Tom

--- ambpdb.f90 2010-02-05 20:10:40.000000000 -0500
+++ ambpdb.f90.tom 2010-02-12 17:51:09.000000000 -0500
.@ -762,7 +762,7 @@
                      atom_element(k)
             else if (remediate) then
                write(nf,60) k_print,atnam,lbres(j),j_print, &
- (coords(jc+m),m=1,3),occb,element
+ (coords(jc+m),m=1,3),occb
             else
                write(nf,61) k_print,atnam,lbres(j),j_print, &
                             (coords(jc+m),m=1,3)
.@ -828,7 +828,7 @@
    return

     50 format(3f10.3,3i5,5x,a4,i5,1x,a4)
- 60 format('ATOM',2X,I5,1X,A4,1X,A4,1X, I4,4X,3F8.3,A23,A3)
+ 60 format('ATOM',2X,I5,1X,A4,1X,A4,1X, I4,4X,3F8.3,A23)
     61 format('ATOM',2X,I5,1X,A4,1X,A4,1X, I4,4X,3F8.3)
     65 format('ATOM',2X,I5,1X,A4,1X,A4,1X, I4,4X,3F8.3,2F6.2,I5,1X,A1)
     67 format('HETATM', I5,1X,A4,1X,A4,'G',I4,4X,3F8.3,2F6.2,I5,1X,A1)

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Received on Fri Feb 12 2010 - 15:30:02 PST
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