AMBER Archive (2009)

Subject: [AMBER] parmchk problem

From: isaac sugden (
Date: Tue Aug 04 2009 - 09:12:29 CDT

To the Amber Development Team,
                i am a researcher, attempting to generate a parm7 file, from
a mol2 file of a large (285 atoms), organic molecule, using amber10.
the idea was to generate an frcmod file using parmchk:

>parmchk -i bonded_tmm_1_rs_rs_rr.mol2 -fi mol2 -o

this could hopefully then be used in the following manner:

source leaprc.gaff
        MOL = loadmol2 bonded_tmm_1_rs_rs_rr.mol2
        loadamberparams bonded_tmm_1_rs_rs_rr.frcmod
        saveramberparm MOL bonded_tmm_1_rs_rs_rr.parm7

within tleap.
however, the parmchk step prints a screen of the following:
Info: the atom number exceeds the MAXATOM, reallocate memory automatically

with no frcmod file.
can you help? i patched the bugfix.all file at installation, and analysis of
the mol2 file seems fine.
Isaac Sugden
AMBER mailing list