AMBER Archive (2004)

Subject: Re: AMBER: charge not zero

From: anshul_at_imtech.res.in
Date: Wed Aug 04 2004 - 22:48:11 CDT

Dear Francois,

I tried to send the the data but even after making it in .gz format the
size was large enough to be included in the mailing list. so is there any
other way i can send the data
meanwhile i would also like to ask a few more questions.

1. What i want to do is that, I have to replace some of the aminoacids
from a protein with another aminoacid which is attached with an organic
molecule (lets name this unit as x). Now I prepare the prepin file for
this unit (x). the end group in this unit (end of the aminoacid part) is
protectd with NH Me and ACE. now when i replace the orignal amino acid
with this unit, what should i do to the end group. Should it be emoved and
if yes then do i need to make some adjustments in the charges after its
removal.

2. Should my end group contain the end group or not?

3. Presently I am replacing the aminoacid in InsightII. I manually remove
the orignal amino acid and then form a bond with this unit. I would like
to know if there is any other simpler method to do so.

I shall be thankful to you if you can answer my queries.

thanks in advance

regards,
Anshul Awasthi

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