Re: [AMBER] antechamber: prepgen mainchain file character limit

From: Junmei Wang <>
Date: Fri, 1 Dec 2017 14:35:35 -0500

HI Markus,

Changing the line "char mcfilename[30] = "MAINCHAIN.DAT";" with "char
mc_filename[MAXCHAR];" solves the problem described in your email.

I noticed that your molecule containing two residues. I would like to
recommend to merge the two residues into one to make antechamber run
smoothly. Later on we will improve antechamber to deal with multiple

All the best


On Thu, Nov 30, 2017 at 10:36 AM, Markus Schneider <> wrote:

> Hi all,
> when using prepgen, I found that segfaults and crashes occured for
> certain choices of mainchain files (-m inputs). In fact, prepgen
> reproducibly crashes for me whenever the mainchain path exceeds 32
> characters. The same setup runs fine for shorter file names. Other input
> files could have longer file names and not make a problem. I guess the
> offending line is found in prepgen.c:
> char mcfilename[30] = "MAINCHAIN.DAT";
> All other arrays which contain file names are initialized like
> char mc_filename[MAXCHAR];
> where MAXCHAR is defined as 2048.
> I suspect increasing the size of the mcfilename array to MAXCHAR would
> get rid of the crashes and save some time for others who run into the
> same issue. It would be great if someone could take a look at this.
> Version used was AmberTools16.
> Kind regards,
> Markus
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Received on Fri Dec 01 2017 - 12:00:04 PST
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