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

From: Schröder, David Christopher <>
Date: Tue, 14 May 2019 14:20:27 +0000

Dear Prof Case, dear Pietro Aronica,

Thank you for your prompt answers. I will look deeper into it with your kind input.


Von: Pietro Aronica <>
Gesendet: Dienstag, 14. Mai 2019 10:07
An: Schröder, David Christopher <>
Betreff: Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide

The lib files you created do not specify atom types, charges or even connectivity for your custom residue. They cannot be used as they are.

Follow the instructions in this tutorial

to create custom residue lib files. You need to generate charges and specify atom types, as well as bonding and other parameters. You can use antechamber to get you started.


On 14/5/19 3:57 PM, Schröder, David Christopher wrote:

Dear Amber users,

I was following Tutorial A1 (

to model a cyclic peptide containing a para connected benzoicacid moiety at C7 position of a tryptophan.

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, furthermore the sequence

command also does not work.

I would be grateful for some help. It might be important to note that I am kind of new to amber in general.

Best regards,



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