On Wed, Sep 26, 2012, Buback, Clayton (S&T-Student) wrote:
> When attempting to run "loadmol2" on my mol2 file (attached), I get the
> following error:
>
> "Fatal Error: last line read: 1 C1 -0.3770 0.4960 -1.4850 c 1 0.816500"
>
Your mol2 file is missing the unit name, which should be on line 2, and also
needs to be on the ATOM lines. For example, look at
$AMBERHOME/AmberTools/test/antechamber/tp/tp.mol2.save:
.<TRIPOS>MOLECULE
TP
13 13 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 CG -1.9590 0.1020 0.7950 ca 1 TP -0.132000
2 CD1 -1.2490 0.6020 -0.3030 ca 1 TP -0.113000
3 CD2 -2.0710 0.8650 1.9630 ca 1 TP 0.015900
....
You are missing the "TP" part. It's not clear how you made the mol2 file,
or why it might be missing these required parts. You might need to use the
-rn flag to set a residue name, but in most cases your should get the default
"MOL" if you don't.
This might be related to other problems you had with antechamber. Try to
re-run the way you made the mol2 file, paying careful attention to the exact
sequence of commands and the presence/absence of the residue name. If there
is a reproducible sequence of commands that makes bad mol2 files, we need to
fix that. But we would need your help in identifying exactly what is going
on.
....dac
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Received on Wed Sep 26 2012 - 15:30:02 PDT
