[gmx-users] Charmm to Gromacs: Polyols force field [Justin]

Mark Abraham mark.abraham at anu.edu.au
Mon Aug 23 18:27:24 CEST 2010

----- Original Message -----
From: Eudes Fileti <fileti at ufabc.edu.br>
Date: Tuesday, August 24, 2010 2:12
Subject: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]
To: gmx-users at gromacs.org

> Hello Justin, thanks again.> Well, the line 40 is just one of the 36 parameters not found!> In this link ( https://sites.google.com/site/fileti/ ) I put the complete files.  > I know I need to determine which bond type should be called and I believe > that it has been done, but I don't know why it's not being found.

You've got heaps more problems than that. The file you say is ffbonded.itp is different from the one grompp is finding, because yours doesn't have 1492 lines in it, and grompp says there's an error there.

I suspect you've started editing in your installation share/gromacs/top folder and gotten things confused. It will be best to start afresh with a fresh installation (and thus copy of share/gromacs/top). Or CHARMM in beta3 is badly broken somehow...

> The order of atoms in the link could be the cause of error?  > Ie, CA-CB would be different from CB-CA, or HO-OH-CB would be different from CB-OH-HO?

No, grompp deals with atom order sensibly.

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