[gmx-users] KALP-15 in DPPC tutorial

[Justin Lemkul]

On 10/16/13 11:29 AM, Sathya wrote:
> Hi,
>
>      I am new gromacs user. Now I am learning gromacs using KALP-15 in DPPC
> tutorial.
>
>      Before Equilibration  the following command is used.
>                    >>make_ndx -f em.gro -o index.ndx
>
> In the tutorial it has been described to Merge the Protein and DPPC groups
> by entering "1 | 13" at the make_ndx prompt.
> But I got only the following options.
>
>    0 System              : 26662 atoms
>    1 Protein             :   138 atoms
>    2 Protein-H           :   109 atoms
>    3 C-alpha             :    16 atoms
>    4 Backbone            :    48 atoms
>    5 MainChain           :    64 atoms
>    6 MainChain+Cb        :    78 atoms
>    7 MainChain+H         :    81 atoms
>    8 SideChain           :    57 atoms
>    9 SideChain-H         :    45 atoms
>   10 Prot-Masses         :   138 atoms
>   11 non-Protein         : 26524 atoms
>   12 Water               : 26520 atoms
>   13 SOL                 : 26520 atoms
>   14 non-Water           :   142 atoms
>   15 Ion                 :     4 atoms
>   16 CL                  :     4 atoms
>   17 Water_and_ions      : 26524 atoms
>
> But i didnt get the option as DPPC in the above.
> I have selected non-Protein hence the grompp which follows this step fails..
> Please help me .. where is the problem, which option to select and how to
> solve this..

Your system has no DPPC in it, so you built it wrong.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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