It seems that the bonds I presumed were missing actually do exist in the prmtop file. The problem seems to occur when I convert this prmtop file (with the corresponding inpcrd file) into .gro and .top files for use in gromacs, again with ParmEd. The .top file contains all the bonds and parameters I need but loading the .gro into a couple different guis (PyMOL, jmol, vmd) all show that my silver containing bonds don't exist, and the silver atom is floating non-bonded in space.
I'm assuming that this isn't an error with ParmEd and might be something I'd need to talk to the GROMACS guys about?
________________________________
From: Kenneth Huang <khuang8.student.gsu.edu>
Sent: 03 February 2022 19:19
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Modifying prmtop/inpcrd files
I'll also tack on that that you can also feed parmed input scripts in the same way you can tleap/cpptraj, ie
cat >pamed.in<<EOF
parm test.prmtop
addDihedral :9.N1 :1.C6 :1.C5 :1.C4 0.0 2.0 1.2
setBond :9.N1 :10.CA 15.0 1.5
parmout newparm.prmtop
go
EOF
parmed -i parmed.in
Which is handy when you have to batch edit things.
Best,
Kenneth
________________________________
From: Sam Walsworth (Researcher) <Sam.Walsworth.hud.ac.uk>
Sent: Thursday, February 3, 2022 1:49 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Modifying prmtop/inpcrd files
Yes, that seems to have worked, thank you.
Sam
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: 03 February 2022 17:54
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Modifying prmtop/inpcrd files
On Thu, Feb 03, 2022, Sam Walsworth (Researcher) wrote:
> raise PackageNotFoundError(name)
>importlib.metadata.PackageNotFoundError: ParmEd
Most likely, you need to "source $AMBERHOME/amber.sh", which should set up the
proper PYTHONPATH. Put this command in your startup scripts (e.g.
~/.bashrc) if you want it done every time you login.
....dac
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Received on Thu Feb 03 2022 - 13:00:02 PST
