Import PDB of Polymer, Error "does not occur in chemistries"

EMC
1

Goal

I’m attempting to import a pdb of a polymer (also built with emc) and then hydrate it. I expect this should be possible given the “import mode=pdb” option and the comments relating to proteins in another post.

Unfortunately the only example with the option, import, relates to a surface, where the chemistry is explicitly defined. I expect that in a protein example a SMILES definition isn’t expected.

I would prefer to avoid redefining the polymer in a SMILES string and import it so that the polymer has the same conformation. As a next step I will be changing functional groups, so again I would prefer to keep the same conformation.

It would be nice if mol2 files could be imported since they are an export option in Avogadro

Input

chemistry file:

#!/usr/bin/env emc_setup.pl

ITEM	OPTIONS

project		membrane
replace		true
field		opls-aa
ntotal		200
mass        true
phases      poly,water
build_order sequence
percolate	true

ITEM	END

ITEM	GROUPS

W   		O

ITEM	END

ITEM	CLUSTERS

poly		import, name="polymer", mode=pdb, type=structure, 1 0.88
water		W 0.12

ITEM	END

There is a psf file in the same directory as the pdb file with the same name.

Output

EMC Setup v4.1.5 (August 1, 2023), (c) 2004-2023 Pieter J. in 't Veld

Info: reading script from "./polymer.esh"
Error: cluster 'poly': does not occur in chemistries
2

Hi Jennifer,

Without knowing what kind of polymer you are actually trying to import, I would suggest using the emc format for exporting from EMC and importing back into EMC. Currently, EMC exports to either PDB (with .pdb and .psf extensions), InsightII (with .car and .mdf extensions), LAMMPS (with .data and .params extensions) and EMC native format (with a .emc extension). Both PDB and LAMMPS formats only contain elemental and connectivity information, where InsightII also includes bond order information. In both cases, EMC will estimate the corresponding groups and SMILES information. This process is somewhat ‘experimental’, meaning that a number of assumptions are made, which not necessarily will lead to the expected result. I would suggest using the EMC format as an exchange format, if you create your import with EMC anyway.

EMC Setup by default outputs both PDB and EMC formats, but also allows for output to InsightII format, all of which are controlled by the options section:

ITEM	OPTIONS

emc		true
insight	true
pdb		true

ITEM	END

Alternatively, you can convert your already existing EMC output (ending in .emc) to either .pdb, .data, or .car using the scripts emc2pdb.emc, emc2lammps.emc, or emc2insight.emc respectively. These scripts can be found in $EMC_ROOT/scripts.