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Squaric Acid: non-carbonyl double bond in 4-membered ring no
#37925 06/11/20 11:30 PM
Joined: Jun 2020
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G
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Hello Everyone,

I am trying to build CHARMM36 parameters for a molecular dynamics simulation using GROMACS. One particular part of this molecule seems to causing the following error:

attype warning: non-carbonyl double bond in 4-membered ring not supported;

I'm having issues uploading so I will post the mol2 file below:

# Molecule Name
# Created by GaussView 5.0.9
#

#
#

@MOLECULE
Molecule Name
12 12
SMALL
NO_CHARGES


@ATOM
1 C1 -2.2070 1.0260 0.0000 C
2 C2 -0.9900 0.3360 0.0000 C
3 C3 0.3260 0.9780 0.0000 C
4 C4 -0.3260 -0.9780 -0.0000 C
5 C5 0.9900 -0.3360 -0.0000 C
6 O6 -0.6580 -2.1670 -0.0000 O
7 O7 0.6580 2.1670 0.0000 O
8 C8 2.2070 -1.0260 -0.0000 C
9 H9 -2.0710 2.1050 -0.0000 H
10 H10 2.0710 -2.1050 0.0000 H
11 H11 -3.2149 0.6669 0.0008 H
12 H12 3.0940 -0.7100 -0.0007 H
@BOND
1 1 2 2
2 1 9 1
3 1 11 1
4 2 3 1
5 2 4 1
6 3 5 1
7 3 7 2
8 4 5 2
9 4 6 1
10 5 8 1
11 8 10 1
12 8 12 1


I have searched this error term and I saw no related thread so I apologize if this has been addressed.

The nature of the rest of the molecule does not allow me to eliminate the double bonds without introducing some charged C atom which then gives me another error:
attype warning: carbon radical, carbocation or carbanion not supported;

What can I do to try and overcome this error? I'm basically forced to have one of these two errors without adding some H, but I can't do that here.

Thank you,


German Barcenas (he/him/his)
Boise State University
Ph.D Student | Materials Science and Engineering
Materials Modeling and Theory Group
germanbarcenas@u.boisestate.edu
Re: Squaric Acid: non-carbonyl double bond in 4-membered ring no
German Barcenas #37928 06/12/20 08:12 PM
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Posts: 8,470
rmv Online Content
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The CGenFF program was written primarily to accommodate molecules of biological interest, and did not exhaustively consider all possible topologies. That doesn't mean your molecule cannot be added to CHARMM, but you will need to do more of the work for yourself. As often happens with academic codes, the CGenFF program developer is no longer actively involved in the CHARMM community.


Rick Venable
computational chemist

Re: Squaric Acid: non-carbonyl double bond in 4-membered ring no
rmv #37929 06/12/20 10:07 PM
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Thank you for your response Rick. Do you have an suggestions on resources to generate this data myself? I have a general idea of using DFT (I have access to Gaussian16) calculations on these smaller subsets of topologies that make up that 4-member ring, but I'm having issues finding any clear directions to actually implementing this with the end result being a correctly edited CHARMM FF.


German Barcenas (he/him/his)
Boise State University
Ph.D Student | Materials Science and Engineering
Materials Modeling and Theory Group
germanbarcenas@u.boisestate.edu
Re: Squaric Acid: non-carbonyl double bond in 4-membered ring no
German Barcenas #37930 06/12/20 11:02 PM
Joined: Sep 2003
Posts: 8,470
rmv Online Content
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I've not done this myself, but I know charges are typically done via HF 6-31g* and scaled for water interactions, and dihedrals use fairly highly levels of theory and basis sets. There are a number of papers from Alex MacKerell's lab that you should probably read.


Rick Venable
computational chemist


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