I've modified the fileleaprc.ff99 file, and it now adds lots of atoms when I
load it.
I'm now having problems with the bond command. My DNA is made of adenine
and thymine bases. The format I tried to use to bond the atoms is
bond ade.1.P ade.94.O3T
bond thy.95.P thy.188.O3T
(ie ade for adenine 1 for the base number and P for the atom name)
but this doesn't work. It doesn't recognise this format. I'm not sure what
I'm doing wrong. I'd appreciate any advice.
Flora
>From: "f m" <floramactavish.hotmail.com>
>Reply-To: amber.scripps.edu
>To: amber.scripps.edu
>Subject: Re: AMBER: Ringof dna
>Date: Thu, 13 Jul 2006 17:00:48 +0000
>
>Thankyou, I'll try that!
>
>Flora
>
>
>>From: "David A. Case" <case.scripps.edu>
>>Reply-To: amber.scripps.edu
>>To: amber.scripps.edu
>>Subject: Re: AMBER: Ringof dna
>>Date: Thu, 13 Jul 2006 09:54:07 -0700
>>
>>On Thu, Jul 13, 2006, Flora Mactavish wrote:
>>
>> > I am attempting to use amber to analyse a ring of dna.
>> >
>> > Is there a command to tell Amber that it is dealing with a ring, or any
>>way
>> > around this problem?
>>
>>You have to modify the leaprc file to do this. Make a copy of whatever
>>you
>>are using (probalby leaprc.ff94 or leaprc.ff99) , and look at the
>>addPdbResMap
>>section. At the bottom of this section are commands that make the default
>>first residue a "5" and the default final residue a "3"-type residue. You
>>don't want that for a circle -- you could actually remove the entire
>>addPdbResMap section for your copy, and load that instead of the default
>>one.
>>
>>Don't forget to use the "bond" command to add the bond between the first
>>and
>>last residues of the circle.
>>
>>...good luck...dac
>>
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>
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Received on Sun Jul 16 2006 - 06:07:07 PDT
