Re: [AMBER] Help with parameterization of non-standard amino acid

From: David A Case <>
Date: Wed, 4 Nov 2020 08:15:40 -0500

On Wed, Nov 04, 2020, Amit Sharma (Asstt. Prof., MCARS) wrote:
>> source leaprc.protein.ff14SB
>> source leaprc.gaff
>> com = loadpdb CFN.pdb
>> chig = sequence { ACE com NME }

Above is incomplete. You need to load the CFN residue by using a command
like "loadOff CFN.lib" or "CFN = loadMol2 CFN.mol2" After one of these
commands, type "list" to be sure that you have a CFN unit loaded, and
use the "desc" command to look at what is inside it, especially at the
head and tail properties. Compare the description of CFN to what you
get for ALA (say), to see what an amino acid unit is supposed to look

Then your sequence command would look like "sequence { ACE CFN NME }"

...hope this helps....dac

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Received on Wed Nov 04 2020 - 05:30:03 PST
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