[gmx-users] Question Regarding GMX Grompp Unknown Atom Type
jalemkul at vt.edu
Thu Feb 9 23:04:21 CET 2017
On 2/9/17 4:58 PM, Elise White wrote:
> 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
> 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).
> ; 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.
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
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