Re: [AMBER] no bonds formed between AA and non-standard residue

From: Vaibhav Dixit <>
Date: Thu, 20 Feb 2020 09:16:46 +0900

Dear All (and David),
I tried the following but still can't get rid of the long-amide bond.
The residue numbers are correct here and I tried using Amber Mask (sec.
19.1 manual) syntax, but that also gives the same error. vmd still can't
read the rst7 file and pdb (from ampdb shows the long aminde-bond). The
help deletebond command shows the same message as in the manual (below).
Please help me understand the correct mask usage here.

> deletebond 420 421 parm com2.prmtop
Using parm com2.prmtop
*Bad command deleteBond:*
deleteBond <mask1> <mask2>
> outparm com2-1.prmtop com2-1.rst7
> deletebond *:420,421 *parmt com2.prmtop
Bad command deleteBond:
deleteBond <mask1> <mask2>
> help deletebond
deleteBond <mask1> <mask2> [parm <idx>|<name>]

    This action deletes any bonds that occur between the atoms in two masks.

        - <mask1> : Amber mask defining one of the atoms in a bond
        - <mask2> : Amber mask defining the other atom in the bond
        - [verbose] : Print out every bond that is deleted as well as the
                      number of other valence terms that were eliminated.

    All bonds will be matched in which one atom comes from <mask1> and the
    atom comes from <mask2>. This action will also delete any other valence
    (like angles and dihedrals) that would get severed by the deletion of
one of
    the bonds.


On Wed, Feb 19, 2020 at 10:56 PM David A Case <>

> On Wed, Feb 19, 2020, Vaibhav Dixit wrote:
> >I removed the TER card between residues 420 and 421, then used bond
> command
> >as shown below.
> >This has bonded the non-std residue CYS-HEM with main chain as expected.
> >tleap adds amide bond between 420 and 421, which I want to delete using
> >parmed deletebond command.
> >> deleteBond :420,421
> >Bad command deleteBond:
> The deleteBond command requires two masks; type "help deleteBond" to see
> more info.
> ...dac
> _______________________________________________
> AMBER mailing list

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Received on Wed Feb 19 2020 - 20:00:02 PST
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