[gmx-users] CHARMM nonbonded parameters and grompp output

[Mark Abraham]

Justin A. Lemkul wrote:

>>> The ffcharmmnb.itp file is incomplete, and I suspect ffcharmmbon.itp is as
>> well.
>>>  Any idea what's going on?
>> No, since you haven't said why you think they're incomplete :-)
> 
> Sorry, I sent that a bit too quickly, didn't I?  I suspect ffcharmmnb.itp is
> incomplete because it contains only 40 lines, with C as the first entry and HT
> as the last entry.  There are no entries for any atom types other than carbon
> and hydrogen.

Right, well that is far too short. HT should not even be the final H 
atom-type. The code writes all of the [atomtypes] in the same foreach 
loop, which is just dumping pre-constructed lines of text. The fact that 
this has only written 40 of many more lines suggests the problem is 
external to the script. Full file-system? Killed process? Try again?

> Perhaps ffcharmmbon.itp is alright - 1364 lines - entries for bonds, angles,
> Urey-Bradley potentials, dihedrals, and impropers.  I just assumed something
> had gone wrong because as soon as I got the message I mentioned, the script
> stopped running.

Yes that file is fine - it gets written before the other.

> The input to the script was par_all27_prot_lipid.prm (that might be important
> information that I also failed to mention before).

Useful information. This is the version I designed the method using, so 
it ought to work perfectly, unless the above file has been modified :-)

Mark