[gmx-users] Question Regarding GMX Grompp Unknown Atom Type

Piggot T. 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

Hello again,

I was amidst inserting a protein into a POPG lipid bilayer using the
Gromos96 53a6
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
to accommodate
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
accommodate it.

[ 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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