AMBER Archive (2009)

Subject: Re: [AMBER] parmchk problem

From: isaac sugden (isaacsugden_at_googlemail.com)
Date: Wed Aug 05 2009 - 12:21:53 CDT

yeah ok, it was created via another program, (aten), as antechamber produced
the following msg when trying to create from a pdb file which i have also
attached:
antechamber -i tmm_rs_rs_rr.pdb -fi pdb -o tmm_rs_rs_rr.mol2 -fo mol2

The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically

Info: the atom number exceeds the MAXATOM, reallocate memory automatically
For atom[37]:O, the best APS is not zero, bonds involved by this atom are
frozen

The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8 (aromatic
double)Error: cannot run "/home/user/Desktop/andy_amber/amber10/bin/bondtype
-j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit

is this perhaps the root problem? i was hoping it might have been a case of
simply editing either the pdb or mol2 file, apologies for the confusion.

On Wed, Aug 5, 2009 at 5:36 PM, case <case_at_biomaps.rutgers.edu> wrote:

> On Tue, Aug 04, 2009, isaac sugden wrote:
>
> >
> > >parmchk -i bonded_tmm_1_rs_rs_rr.mol2 -fi mol2 -o
> > bonded_tmm_1_rs_rs_rr.frcmod
>
> First: how was the input mol2 file generated? (It needs to have been
> constructed with antechamber.)
>
> Second, please post the input mol2 file...it's not possible to figure out
> the
> problem (no frcmod output) without more information.
>
> ....dac
>
>
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