[gmx-users] Question Regarding GMX Grompp Unknown Atom Type
T.Piggot at soton.ac.uk
Thu Feb 9 20:48:42 CET 2017
Where did you obtain the POPG lipid topology from? From what I can remember, this looks like the Elmore Berger based parameters. You need to have the appropriate corresponding entries for all the itp atomtypes in your force field files. That said, (if I've got the correct force field you are using) this force field doesn't perform very well for PG (see http://pubs.acs.org/doi/abs/10.1021/jp900645z). If you want to use a GROMOS based force field, the only parameters I'm aware of that work at least reasonably well are some of my GROMOS-CKP ones (see http://pubs.acs.org/doi/suppl/10.1021/jp207013v for a bit more info; the parameters should be available on the Lipidbook website). If you have more flexibility in terms of force field, CHARMM36 and Slipids should work well (amongst others).
It's probably also worth pointing out that the GROMOS 53A6 protein force field isn't that great in certain circumstances (e.g. unstable for short helices). You'd be better off with a different GROMOS protein force field too (e.g. 54A7). Or, indeed, a recent CHARMM/AMBER force field with an aforementioned lipid model.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Elise White [elisenwhite at gmail.com]
Sent: 09 February 2017 15:54
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Question Regarding GMX Grompp Unknown Atom Type
I was amidst inserting a protein into a POPG lipid bilayer using the
force field when I ran into a rather tricky problem -
An error message popped up that said, "Unknown atom type: HO."
I have performed all the modifications necessary to expand my force field
the lipid bilayer, and this atom type does not seem to appear anywhere
under my bilayer's 'atom types' heading, 'non bond param' heading or 'pair
type' heading in the ffnonbonded.itp file.
I did notice, however, that this atom type does appear twice in my lipid
bilayer's topology file and
I am wondering if you have any suggestions as to how to either remove it or
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 HO 1 POPG H1 0 0.3980 1.0080 ;
2 OA 1 POPG O2 0 -0.5480 15.9994 ;
3 HO 1 POPG H3 1 0.3980 1.0080 ;
4 CH2 1 POPG C4 0 0.1500 14.0270 ;
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