[AMBER] saquinavir.prep

From: andrea <andrea.spitaleri.iit.it>
Date: Thu, 14 Nov 2013 12:26:01 +0100

Hi there,

I have a quick question about the saquinavir.prep

This file is composed by 5 different unit names (the saquinavir in the
original paper has been
split in 5 different portion to perform charge calculations). My aim is
to regenerate the OFF lib file and the prmtop file for the whole
reconstituted molecule. I read about sequence and combine keywords but
basically I do not know the proper procedure to follow.
I run loadamberprep SQV.prep but in the list only the first unit name
DIQ is loaded. Then:

saveoff DIQ diq.lib

produce the OFF lib for DIQ portion. Do I need to split the SQV.prep in
5 different prep files and load them all? Once I get the list of the
five unit names how to "combine" them in order to get the OFF lib and
prmtop file for the whole molecule?

I could not find any help from the previous posts in the mailing list.

thanks a lot in advance


Andrea Spitaleri PhD
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
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Received on Thu Nov 14 2013 - 03:30:03 PST
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