[gmx-users] Error 'Atomtype NTL not found'

[Justin Lemkul]

On 5/15/15 4:15 PM, Ta-Chou 黃大周 wrote:
> Dear all,
>
> Actually, I had google for this error message, but I can't understand the
> answer clearly, and it seems the previous question didn't finish yet.
>
> I want to run a MD simulation with amber force field for a membrane protein.
> And the simulation box contains my goal membrane protein, POPC lipid and
> water, later will add ions.
> I choose the force field: amber99sb-ildn, and download the POPC.itp file
> from this website:
> http://bioinf.modares.ac.ir/software/mb/lipid_topology_files.htm
>
> In my top file, which will use in later grompp command.
> Top file as below:
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
> #include "POPC.itp"
>
> ; Include chain topologies
> #include "tm_Protein.itp"
> #include "tm_Protein2.itp"
> #include "tm_Protein3.itp"
> #include "tm_Protein4.itp"
>
> ; Include water topology
> #include "amber99sb-ildn.ff/spce.itp"
>
> ; Include topology for ions
> #include "amber99sb-ildn.ff/ions.itp"
> ...
>
> After I type grompp command, it shows the error 'Atomtype NTL not found.'
> I found that the NTL atom-type showed in POPC.itp file.
> Can anybody help me to fix this problem? Or I should modify this itp file?
>

Apparently you have to also download their Amber/Slipid force field archive to 
get all the parameters for those atom types.  Then you'll somehow have to 
combine all that into one functional force field.

-Justin

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

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

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