Re: [AMBER] Improper torsion terms when building covalent bond in leap

From: He, Amy via AMBER <amber.ambermd.org>
Date: Tue, 27 Feb 2024 02:05:03 +0000

Hi Nicole,

I have done similar things before and these specifications worked for me, when I added them in the parameter modification (.frcmod) files. I was doing that because part of my system could not be typed by the standard force field. I did not modify the main parameter (.dat) file.

The beginning of my tleap input is like:

source leaprc.<some standard force field>
source leaprc.gaff2
loadamberprep <for the modified residues>.prepi
loadamberparams <for the modified residues>.frcmod
loadamberparams <parameters specified by mixed types>.frcmod

It also worked when I combined the two .frcmod files into one.

Hope this helps! 


--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: Nicole Vita via AMBER <amber.ambermd.org>
Date: Monday, February 26, 2024 at 7:18 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Improper torsion terms when building covalent bond in leap
Hi,
I am trying to parameterize a covalent bond and am having problems with my torsion terms.
I was able to fix and add all the terms into the *.frcmod file that were missing except for one.
The following term continues to give me an error:
      Error:  ** No torsion terms for atom types: CO-O2-c3-hc
        for atom CG at position 5.699000, -24.112000, 5.185000,
            atom OD2 at position 6.946000, -24.383000, 5.605000,
            atom C55 at position 7.254000, -24.434000, 6.997000,
        and atom HC55 at position 6.327000, -24.636000, 7.534000.
I went into the gaff2.dat file and tried multiple terms but the terms I added thinking they were the closest representation were:
                CO-O2-c3-hc   2    5.400       180.000           2.000      same as X -c -os-X
However, I am still getting the torsion term error when trying to write the *.inpcrd file.
Any help to solve this problem would be greatly appreciated.
Cheers,
Nicole
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Received on Mon Feb 26 2024 - 18:30:01 PST
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