Sorry, there was a typo in my previous reply, I meant .frcmod file (not .fomcrd!)
Ibrahim
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Saturday, October 8, 2022 9:35 PM
To: Moustafa, Ibrahim M. <ria2.psu.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] parameterization for non-standard nucleotide
On Sat, Oct 08, 2022, Moustafa, Ibrahim M. via AMBER wrote:
>
>set model head model.DXC.P
>saveoff model newresidue.lib
>
>The commands work. But when I tried to check the created library in tleap
>again I don't see the Head information in the saved .lib file.
Before or after the saveoff command, you could use the desc command in tleap
to see what is in the unit; eg. "desc model.DXC". (Is this what you meant
when you say "check the created library in tleap"?)
>loadoff ./newresidue.lib
>model = loadpdb "./complex.pdb"
As Maria noted, it is likely that the residue or atom names in complex.pdb
don't match those in newresidue.lib. In tleap, use the "list" command to
see what units are loaded, and "desc" command to see the properties of the
units that you have. Using a text editor is generally the easiest way to
examine the pdb file.
...hope this helps. If not, you may have to explain how you made the new
unit, probably posting the newresidue.lib file.
....dac
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Received on Sat Oct 08 2022 - 21:30:03 PDT
