AMBER Archive (2007)

Subject: AMBER: assigning of head atom as null.

From: SHARAD gupta (sharadguptaacbr_at_yahoo.co.in)
Date: Tue May 15 2007 - 02:26:23 CDT

Dear List
              
I am new to amber and want to simulate modified DNA
Duplex. For this I have prepared respective modified
monomers and assigned RESP charges using Gaussian
programme but the problem comes with terminal
monomers. I am unable to assign the head and tail atom
as null for N-terminal and C-terminal residues
respectively by using mainchain file.
In the mainchain file, i am using HEAD_ATOM null
for N terminal residue.
and TAIL_ATOM null for C-terminal residue.
I thing the way i am using, to assign null atom is not
right. Can we do this by using set commands.
Can anyone suggest me the correct path, It would be a
great help.

Thanks

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Sharad Kumar Gupta
Senior Research Fellow
Dr. B. R. Ambedkar Center for Biomedical Research
University of Delhi
Delhi-10007
INDIA
   
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