Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide

From: David A Case <>
Date: Tue, 14 May 2019 09:12:31 -0400

On Tue, May 14, 2019, Schröder, David Christopher wrote:
>The sequence is as following: cyclo Trp (7-4Benzoic acid) VAL ARG GLY ASP
>I took a pdb file of the molecule with initial coordinates and cut off
>the modified Trp and the benzoic acid part, renamed all atoms
>and created from these fragment-pdbs lib files following the
>tutorial. Please find the files attached.
>When I load these lib files in leap they are not listed when using the
>list command....

Your .lib files have the name of the residue always as "mol". You need
to edit this to make it be the residue name you want. (You will either
need to remake the library files specifying the correct residue name, or
use an editor to change "mol" everywhere to what you want it to be.

You might still get problems later on, but tleap should now recognize
your molecules.

....good luck...dac

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Received on Tue May 14 2019 - 06:30:03 PDT
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