[gmx-users] About Area per lipid using Gid-MAT Continuation...

[Justin Lemkul]

Please send me the coordinate and input files off-list.

-Justin

On 11/17/16 11:40 AM, Poncho Arvayo Zatarain wrote:
> Hello Justin: Following with the error on my Grid-MAT-MD.pl line 761. This is my param_exampe using in Grid-MAT for calculate area per lipid in DPPC/DPPE bilayer
>
>
> Input file and input file parameters
>
> coord_file:         dppc128+dppe128+hlt+tip3.gro
>
> file_type:           gro
>
> num_frames:    1
>
> num_lipid_types:  2
>
> resname1:          DPPC
>
> atomname1:         P8
>
> resname2:           DPPE
>
> atomname2:         P8
>
> Solvent:                 TIP3
>
>
> Define the size and shape of the grid
>
> box_size: Vectors
>
> #override_vectors: 8.83600, 8.83600, 7.90000
>
> grid: 100
>
> conserve_ratio: yes
>
>
> Define whether there is a protein embedded in the bilayer
>
> protein: yes
>
> precision: 1.3
>
> value: 5.0
>
>
> Defined the desire output files and format
>
> output_prefix: output
>
> output_format: vector
>
> thickness: yes
>
> area: yes
>
> top_pbc: yes
>
> bottom_pbc: yes
>
> average_pbc: yes
>
> top_areas: yes
>
> bottom_areas: yes
>
>
>

-- 
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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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