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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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