RE: Re: Problems to parametrize molecules

From: Bennion, Brian (
Date: Fri Apr 24 2015 - 13:46:52 CDT

Hello Evandro,

These are the steps that I followed.
1. I took your mol2 file and submitted it to
Amazingly the server returned an str file with extremely low penalties for nearly all the atoms.
There are a few that will need some work (more on that later).
2. I converted all the UNK and b_list names to EVA in the MOL2 file and STR file.
3. I converted the mol2 file to a pdb with babel -imol2 b_list.mol2 -opdb b_list.pdb
4. I loaded this pdb file in to vmd192
5. I used the molfacture plugin to add the correct atom type (very tedious but critical).
6. I saved the psf and pdb and top files from molefacture.
7. Now you can use FFTK to validate the very few missing parameters. I would recommend doing this by reloading the psf and pdb files in to vmd and using molefacture to cut the pieces out to make the calculations smaller. That is cut out the biphenyl and piperazine portions of your molecule to validate the charges and angle that is noted in the STR file.
Now unless you have access to gaussian you will be stopped at this point and will need to judge whether the penalties are such you can live with them (and the reviewers as well) or find access to gaussian by paying for it or collaborating with someone.

Have a good weekend.

From: Evandro Semighini []
Sent: Friday, April 24, 2015 10:49 AM
To: Bennion, Brian
Cc:; Mayne, Christopher G
Subject: Re: namd-l: Re: Problems to parametrize molecules

Hello Brian,

The molecule is attached to the e-mail, in mol2 format.

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:50 CST