[gmx-users] (no subject)

[Mark Abraham]

----- Original Message -----
From: munubas at yahoo.com
Date: Monday, June 28, 2010 5:29
Subject: [gmx-users] (no subject)
To: gmx-users at gromacs.org

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| > Hellow, > My sequence was processed with SPDBV which add NH3 and COO- at the Nterminal and Cterminal respectively thereby MD simulation was carried out using GROMACS versions of  3.3.2 and 4.0.  The system was working well. > Now I would like to add protecting groups i.e.acetyl group (CH3CO) and Nmethyl (NHCH3) at the N and C terminal respectively instead of NH3 and COO- using Gromacs 4.0.  > Kindly suggest me needful action for the said construction. Or kindly suggest the software which can construct like CH3CO-Gly-trp-lys- - - - - - -  - NHCH3 thereby getting output file can be used by GROMACS 4.o for completing my MD of the molecuel having such a sequence any like CH3CO-Gly-trp-lys- - - - - - -  - NHCH3 .

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You will need some non-GROMACS software to do this. Some suggestions are here http://www.gromacs.org/Documentation/File_Formats/Coordinate_File

Mark

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