Re: [AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT

From: Scott Brozell <sbrozell.rci.rutgers.edu>
Date: Tue, 8 Aug 2017 17:22:54 -0400

Hi,

On Tue, Aug 08, 2017 at 12:51:44AM +0000, Tsai Kun-Lin wrote:
>
> I am using AmberTools17 and try to parameterize a drug like molecule using antechamber and parmchk2 with gaff2. The followings are the commands I use:
> antechamber -i Structure3D.sdf -fi sdf -rn LIG -o Structure3D.mol2 -fo mol2 -c bcc -nc 0 -pf yes -dr no -at gaff2
>
> parmchk2 -i Structure3D.mol2 -f mol2 -o Structure3D.frcmod -s 2
>
> The first command finished successfully, however, the second command returned me an error message and an empty frcmod file:
>
> Warning: Atom type (cs) is not in PARMCHK.DAT; using default values
> for improper_flag [0], group_id [0], and equivalent_flag [0].
> It is recommended to add the new atom type (cs) to PARMCHK.DAT.
> Segmentation fault (core dumped)

Using an up to date patched AmberTools 17, when i run the parmchk2
command above on the mol2 file created by the first command it produces
the attached Structure3D.frcmod without complaint.

In addition, valgrind does not report a problem.

You could rebuild antechamber with debugging symbols and report the trace:
cd AmberTools/src/antechamber/
make AMBERBUILDFLAGS='-g'
parmchk2 -i Structure3D.mol2 -f mol2 -o Structure3D.frcmod -s 2

And you could investigate your AmberTools installation:
./update_amber --show-applied-patches
cd AmberTools/test/antechamber/
make
make check

scott



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Received on Tue Aug 08 2017 - 14:30:03 PDT
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