Re: [AMBER] Amber10 Installation

From: sikander azam <syedazam2008.gmail.com> Date: Mon, 25 Jan 2010 09:08:54 -0500

---
> ESC[?1034h[gtkleap]$ set default echo on
---------------------------------------
possible FAILURE:  check box.out.dif
/home/ssa/amber11/test/sleap/prmtop
1c1
< [gtkleap]$ set default echo on
---
> ESC[?1034h[gtkleap]$ set default echo on
---------------------------------------
possible FAILURE:  check leap.out.dif
/home/ssa/amber11/test/sleap/molinfo
1c1
< [gtkleap]$ set default echo on
---
> ESC[?1034h[gtkleap]$ set default echo on
---------------------------------------
possible FAILURE:  check 132d.mol2.dif
/home/ssa/amber11/test/sleap/DNA
1583c1583
<        1       DG
---
>        1      DG5
1594,1595c1594,1595
<       12       DC
<       13       DG
---
>       12      DC3
>       13      DG5
1606c1606
<       24       DC
---
>       24      DC3
---------------------------------------
possible FAILURE:  check test1.out.dif
/home/ssa/amber11/test/sleap/propdiol
1c1
< [gtkleap]$ set default echo on
---
> ESC[?1034h[gtkleap]$ set default echo on
---------------------------------------
possible FAILURE:  check test2.out.dif
/home/ssa/amber11/test/sleap/propdiol
1c1
< [gtkleap]$ set default echo on
---
> ESC[?1034h[gtkleap]$ set default echo on
---------------------------------------
possible FAILURE:  check first.pdb.dif
/home/ssa/amber11/test/ambpdb_first_protein
2147c2147
< HETATM 2145  X   BMH G  62      29.312  38.819  37.740  0.  0.   62 N
---
> HETATM 2145  X   BMH G  62      29.313  38.819  37.740  0.  0.   62 N
*
Though I checked xleap it was running well.
Kindly look into it*
On Sat, Jan 23, 2010 at 9:48 AM, David Watson <dewatson.olemiss.edu> wrote:
> You're AMBERHOME seems to be set very wrong.
> It should probably be something like
>   /home/ssa/amber11
> but, as it stands, you have it set to
>    /home/ssa/amber11//home/ssa/amber11//home/ssa/amber11
>
> You may want to
>   cd /home/ssa/amber11/src
>   make -f Makefile_at realclean
>   export AMBERHOME=/home/ssa/amber11
>   ./configure_at gnu
>   make -f Makefile_at
> Then follow the remainder of the AmberTools installation instructions in
> section 1.2 of the manual.
>
> On Jan 23, 2010, at 6:23 AM, sikander azam wrote:
>
> > ptraj: analyze fluctuation matrices
> > diffing 1rrb_vac_distmat.dat.save with 1rrb_vac_distmat.dat
> > awk: fatal: can't open source file
> >
> `/home/ssa/amber11//home/ssa/amber11//home/ssa/amber11/bin/bin/test/ndiff.awk'
> > for reading (No such file or directory)
> > possible FAILURE:  check 1rrb_vac_distmat.dat.dif
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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