On Fri, Oct 1, 2010 at 1:35 PM, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Oct 01, 2010, Francesco Pietra wrote:
>
>> At a fresh check this morning, the residue number 4 in the for-last
>> column of the mol2 file was the problem. Replacing 4 with 1, the mol2
>> file was loaded by xleap. Now I'll see if I can build prmtop/inpcrd
>> for the peptide.
>
> This sounds like bugfix 10 to version 1.2 has not been applied. If that is
> the case, it's probably worth upgrading to the latest version.
Recompiled ambertools.1.2/gcc for current bugfix.all and amber.10/gfortran.
Reprepared pha.mol2 with new antechamber and pha.frcmod with new parmchk.
$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leapcrd.ff99SB
source leaprc.gaff
x = loadmol2 pha.mol2 (where pha.mol2 has PHA residue numbered 4 like
in the mol2 file that I showed before) (same as previously, apart very
slight differences in the charge values)
xleap crashed. Such a crash was an alternative to hanging, i.e. one of
the two occurred, even on previous attempts with older compilation of
ambertools.1.2.
As sustiva.mol2 (tutorial b4) is treated correctly by xleap, there
must be something wrong in pha.mol2 . Such oddness is not detected by
VMD. It also opens correctly, although currently Chimera treats by
pseudobonds the aromatic rings in mol2 files.
As to now I have no better ideas.
Thanks
francesco
>
> ....dac
>
>
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Received on Sun Oct 03 2010 - 15:00:03 PDT
