Read pdb/xyz/mol2 structure instead of SMILES

EMC
1

Hello Users,

I am interested in generating the amorphous polymer melt using EMC with any atomistic force field (preferably GAFF).

I am having a hard time entering SMILES and wondering if there is any way to input the repeating units/molecule motifs using PDB/XYZ/MOL2 formats.

Thanks,
Karteek

2

Hi Karteek,

Unfortunately, you cannot load your repeat units or molecules through a position-based formats. These formats are much more ambiguous than a SMILES. EMC does read PDB through the import option under ITEM CLUSTER in the chemistry format of EMC Setup, but this is thought to be used for protein structures from the Protein Databank. These structures are static during the build process. Internally a transfer to SMILES is made. The PDB has to come with a PSF. Unfortunately, PSF lacks bond valence information. SMILES is a more concise way to define your chemistry. You can use for instance

If you would like to draw a 2D structure and convert this into SMILES. JChemPaint is a Java-based structure tool.

Pieter

3

Thanks Pieter for the reply.
I will try to use SMILES then.

Could you also help me with other question on EMC_setup.pl. I am using the same syntax as previous version, but newer version gives me an error.

Regards,
Karteek

4

Hi Karteek,

Could you share what you are trying to do?

Pieter

5

Hi Pieter,

Thanks for the response. I am trying to use EMC to generate amorphous polymer electrolyte structures. I have force field generation from other tools. I cannot attach the file as a new user it complains and pasting the contents here.

Secondly, I am also running into another issue while using emc_setup.pl
Command:perl ~/softwares/EMC/v9.4.4/scripts/emc_setup.pl polymer.esh
Error: Undefined subroutine &EMC::IO::open called at /Users/karteek/softwares/EMC/v9.4.4/scripts/emc_setup.pl line 2886.

ITEM OPTIONS

replace true
field opls
density 1.0
pdb_unwrap true
number true
seed 14546272581

ITEM END

ITEM GROUPS

PPS Sc1ccc()cc1,1,PPS:2

ter1 C*,1,PPS:1
ter2 *C,1,PPS:2

ITEM END

Clusters

ITEM CLUSTERS

poly random,2

ITEM END

Polymers

ITEM POLYMERS

poly
100 PPS,20,ter1,1,ter2,1

ITEM END

6

The error you see is caused by adding modules to EMC Setup. Automated recognition of the location of the modules does not seem to work correctly. This can be bypassed by setting the environment variable EMC_ROOT to the directory in which you unpacked your EMC package, e.g. by adding the line

export EMC_ROOT=~/emc/v9.4.4

to your .bashrc. Future EMC versions will have fixed this problem. Pertaining the pasted .esh, I noticed, that the definition of PPS under groups is not complete (I am missing the connectivity asterisks). Could you help me out there?

7

Hi Pieter,

Thanks for all the responses. I am able to use EMC now and do not have further issues.
The Smiles for PPS that worked for me is

PPS c1ccc(S)cc1,1,PPS:2

Thanks,
Karteek

8

Hi Karteek,

Good to hear, that things are working for you. I think, that the SMILES you mean, is represented by

PPS *c1cccc(S*)cc1, 1, PPS:2

The MatSci editor automatically italicizes everything between two asterisks. This can be circumvented by starting a line with four spaces, which induces the code mode.

Pieter