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

Mark Abraham mark.abraham at anu.edu.au
Mon Aug 23 19:40:12 CEST 2010

----- Original Message -----
From: Eudes Fileti <fileti at ufabc.edu.br>
Date: Tuesday, August 24, 2010 3:22
Subject: Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark]
To: gmx-users at gromacs.org

> Hello Mark thanks for the comments,
> In fact, what I did was insert the parameters into ffbonded.itp file. 
> What I presented the link above is just the part that I had added 
> (of course there is the line 1495, not shown!).
> The installation where I started making the change is new, 
> I have not changed anything, just added the lines for the parameters mentioned. 
> Nevertheless, you think I need to re-install the gromacs?

You shouldn't be editing ffbonded.itp directly, because now you've got no way short of a re-installation to go back at start afresh. Instead, copy the whole of charmm27.ff directory to your working directory, and edit *that*. So maybe, you do need to re-install, but perhaps save a copy of what you've already done so far - much of it is probably worthwhile :-)

As Justin's told you, you need to go and look at the lines that grompp is telling you are wrong. You've now shown us inserted bits twice - but those are useless to us because we don't have the context to know which is line 1492. If we were blessed with infinite time and patience, we might spot your problem without the context. However you already have a tool for spotting problems - grompp! So we're not inclined to spend much effort when you can at least identify the offending line for us in about 5 seconds with vi :-) Once you've found the line, check you've formatted it correctly.


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