AMBER Archive (2009)

Subject: Re: [AMBER] How to fix specific atoms? (not residue)

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Sat Jul 11 2009 - 17:01:04 CDT

There are several things wrong or potentially wrong here:

- Some commas are missing.
- You probably want more minimization cycles (maxcyc, ncyc options).
- 500 kcal/mol is quite a lot...
- Did you specify reference coordinates with -ref when invoking sander?

Finally, when asking questions about software difficulties, it's
always a good idea to include the exact error message so others have
an idea what precisely doesn't work.

--Tom

On Sat, Jul 11, 2009 at 7:46 AM, Myeong
Lee<myeong.lee_at_nano.tu-dresden.de> wrote:
> Hi,
>
> I want to hold the specific atoms (not the residues) during minimization
> process.  I don't know what's the keyword for giving restraint for specific
> ATOMS.  In other words, I want to fix only part of the atoms in the same
> residue.
>
> Another option in case I can't fix individual atoms is to hold the atoms
> with atom type "CA".  I tried the following, but didn't work.  (These are
> the atoms which do not belong to DNA/counterion/water)
>
> &cntrl
>  imin   = 1,
>  maxcyc = 4,
>  ncyc   = 1,
>  ntb    = 1,
>  ntr    = 1,
>  cut    = 10.0
>  ntwx   = 100
>  restraint_wt=500.0
>  restraintmask='@CA'
> END
>
> Thanks.
>
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