Missing rules error for simple polymer with OPLS-AA

EMC
1

Hi all,

I am a very new user of EMC and am trying to build polymers representative of anion-exchange membranes similar to this work: https://doi.org/10.1021/acsapm.1c01798. I downloaded EMC on my macOS laptop two weeks ago, so I have the most recent version.

My test system consists of a chain of benzene rings, with the ultimate goal of adding in fluorocarbons and cationic groups at certain sites on the benzenes.

I have tried my simple chain of benzene rings in EMC using the OPLS-UA force field and, as far as I can tell, everything works (using vmd -e command + looking at data file).

When I switch to OPLS-AA, I get the “missing rules” error:

Info: applying '~/emc/v9.4.4/field/opls/2012/opls-aa.prm'

Warning: no rule found for {group, site} = {test, 0}.
Warning: no rule found for {group, site} = {test, 1}.
Warning: no rule found for {group, site} = {test, 2}.
Warning: no rule found for {group, site} = {test, 3}.
Warning: no rule found for {group, site} = {test, 4}.
Warning: no rule found for {group, site} = {test, 5}.
Warning: no rule found for {group, site} = {test, 6}.
Warning: no rule found for {group, site} = {test, 7}.
Warning: no rule found for {group, site} = {test, 8}.
Warning: no rule found for {group, site} = {test, 9}.
Warning: no rule found for {group, site} = {terminator, 0}.
Warning: no rule found for {group, site} = {terminator, 1}.
Warning: no rule found for {group, site} = {terminator, 2}.
Warning: no rule found for {group, site} = {terminator, 3}.
Warning: no rule found for {group, site} = {terminator, 4}.
Warning: no rule found for {group, site} = {terminator, 5}.
Warning: no rule found for {group, site} = {terminator, 6}.
Warning: no rule found for {group, site} = {terminator, 7}.
Warning: no rule found for {group, site} = {terminator, 8}.
Warning: no rule found for {group, site} = {terminator, 9}.
Warning: no rule found for {group, site} = {terminator, 10}.

Error: core/fields.c:433 FieldsApply:

Missing rules.

Program aborted.

I have tried typing my SMILES strings as:

test         *c1ccc*cc1
terminator   *c1ccccc1

but still encounter the same issue. This error has persisted even when I add a methyl group separating the benzene rings (but still runs with OPLS-UA) as I wasn’t 100% sure on my atom type for the benzenoid carbon connecting to the next ring.

Based on the .prm files, it seems that OPLS-AA should have the requisite atom types (ca, ha, ct). I have read through the discussions regarding adding rules to OPLS-AA, but I don’t understand the architecture of the .define, .prm, and .top well enough to fix my own problem. I have copied my input file below as I am not allowed to attach it.

Many thanks in advance for any help!

#!/usr/bin/env emc.pl

# Options

ITEM		OPTIONS

project		benzene_chain
field		opls-aa
#field 		opls-ua
number 		false
ntotal		1000
mass		true
replace		true
#field_debug reduced 

ITEM		END

# Groups

ITEM		GROUPS

test		*c1:cc:c*c:c1, 1, test:2

terminator	*c1:cc:cc:c1, 1, test:1, 1, test:2
#terminator	*c1ccccc1, 1, test:1, 1, test:2

ITEM		END

# Clusters

ITEM		CLUSTERS

poly		alternate,1

ITEM		END

# Polymers

ITEM		POLYMERS

poly
1			test, 5, terminator, 2

ITEM		END
2

Hello,

I was also going to create a similar topic. Since the last release, I cannot build simple polymer (polystyrene) melt with opls-aa. Taking the opls-aa forcefield files from the previous release fix the problem of missing rules, so the problem come from the updated forcefield files.

3

Dear users,

My apologies for the late reply. I have been on vacation for the past three weeks. I was not aware of the issues with OPLS-AA. In the meanwhile, I have created a 2024 version of OPLS-AA, which uses bond increments for partial charge assignment. This allows for a more general and flexible force field. I would suggest to install the following two files

opls-aa.prm (62.2 KB)
opls-aa.top (13.3 KB)

in $EMC_ROOT/field/opls/2024. This allows them to be accessed through field opls/2024/opls-aa as is illustrated by the following example:

# Options section

ITEM	OPTIONS

replace		true
field		opls/2024/opls-aa
density		0.1
radius		10
nrelax		500
number		true
focus		true
pdb_licorice	true
emc_execute	true

ITEM	END	# OPTIONS

# Groups section

ITEM	GROUPS

m1		*c1ccc(cc1)*, 1, m1:2
t1		*c1ccccc1, 1, m1:2
t2		*c1ccccc1, 1, m1:1

ITEM	END	# GROUPS

# Clusters section

ITEM	CLUSTERS

polymer		alternate,1

ITEM	END	# CLUSTERS

# Polymers section

ITEM	POLYMERS

polymer
1		m1,10,t1,1,t2,1

ITEM	END	# POLYMERS

I have increased radius and nrelax since polyphenylene is rather stiff. Note that OPLS-AA has a native type C! for bridging aromatic carbons between two phenyl rings which is captured by type c3ab in OPLS-AA 2024.

I will have to upload a new version of EMC, since the current version does not understand ^6 ring designations in rules well. I will post an update here, once this new version has been uploaded for all compilation targets. This 2024 version of OPLS-AA is still experimental. Please let me know, if you experience any issues.

For the 2012 version of OPLS-AA one can use the files as provided by the 2023 release of EMC:

opls-aa.prm (34.9 KB)
opls-aa.top (30.0 KB)