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.
On Sat, Jul 11, 2009 at 7:46 AM, Myeong
> 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
> 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)
> imin = 1,
> maxcyc = 4,
> ncyc = 1,
> ntb = 1,
> ntr = 1,
> cut = 10.0
> ntwx = 100
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