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

[Justin Lemkul]

On 2/9/17 4:58 PM, Elise White wrote:
> Tom,
>
> I really appreciate your insight into this problem - I did have a look at
> the Lipidbook
> website and downloaded a new lipid bilayer from there. I followed the same
> procedure,
> and now an error regarding my topology syntax has appeared:
>
>
> Fatal error:
>
> Syntax error - File topol_popg.top, line 10
>
> Last line read:
>
> '#include “gromos53a6_atb_popg.ff/forcefield.itp”'
>
> This is what my topology file looks like -
>
> ; Include chain topologies
> #include “gromos53a6_atb_popg.ff/forcefield.itp”
> #include “popg_after40ns.itp”
>

You have two different types of quotation marks in the topology, suggesting that 
you're not using a plain text editor to make alterations.  Curly and straight 
quotation marks are different characters; grompp will choke on the former (as it 
will with bad line endings, etc).

-Justin

> ; Include water topology
> #include "gromos53a6_atb_popg.ff/spc.itp"
>
> ; Include ion topologies
> #include "gromos53a6_atb_popg.ff/ions.itp"
>
> ; System specifications
> [ system ]
> 128-Lipid POPG Bilayer
>
> [ molecules ]
> ; molecule name nr.
> DPO 128
> SOL 3,527
> NA+ 128
>
> I was hoping you might be able to advise me on resolving this issue.
>
> Best,
> Elise
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================