AMBER Archive (2006)

Subject: Re: AMBER: how to do a molecular dynamic study on a trimer

From: Gobind Bisht (gsbisht1_at_gmail.com)
Date: Sat Aug 12 2006 - 12:05:29 CDT

hi Abhilash,
                 I had a similar problem and i figured out that its
important that TER is followed with some blank spaces. I mean instead of
giving newline immediately after typing TER, fill the whole line with blank
spaces. That worked for me atleast.
cheers

On 8/11/06, David A. Case <case_at_scripps.edu> wrote:
>
> On Fri, Aug 11, 2006, Abhilash wrote:
>
> > I have a trimer and wish to do a molecular dynamics study with it. How
> > do I set up amber(amber 8.0) to recognize the three chains of the trimer
> > as distinct units. It treats the trimer as a continuous unit and the
> > last amino acid of the chain A is treated as being bonded to the first
> > amino acid of the chain B.
> > I tried to specify "OXT" and "TER" tags to specify the end of the chains
> > but that does not seem to work in this case.
>
> Add a TER card between chains in the input pdb file in indeed the correct
> thing to do. You'll probably have to give details of what your pdb file
> looks
> like, and what commands you gave to LEaP.
>
> ...dac
>
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-- 
Gobind Singh Bisht
Department Of Biotechnology
IIT Kharagpur, Kharagpur-721302
West Bengal,

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