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
other
atom comes from <mask2>. This action will also delete any other valence
term
(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 <david.case.rutgers.edu>
wrote:
> 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
>
>
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--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
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Received on Wed Feb 19 2020 - 20:00:02 PST
