Hello Seçkin
I think the first thing to do is make sure you have the correct atom types assigned to your nonstandard residue. These are defined in the parameter files located in your $AMBERHOME/dat/leap/parm installation directory. You can also look at similar residues to see how they are defined there for equivalent atoms. Then run this through parmchk again to see if you have less (hopefully) of these lines.
Checking the frcmod output from parmchk and/or optimize the parameters is more difficult. The simplest way to "borrow" parameters from related terms, but this can be dangerous in my opinion. To properly do this will require performing some QM calculations for the internal coordinates that you are interested in and then comparing the resulting energy curves to the output of MM calculations. You might consider using wolf2pack (www.wolf2pack.com) to help guide you in doing this. If the existing molecular database does not contain the internal coordinates you need, then write a post on wolf2pack's message board and I will see what I can do for you. You also might consider using R.E.D. (
http://q4md-forcefieldtools.org/RED/) to help create balanced partial atomic charges for your nonstandard residue.
Cheers,
Karl
----- Original Message -----
From: "seçkin Boz" <bozseckin.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Wednesday, May 8, 2013 11:17:35 AM
Subject: [AMBER] ATTN: need revision
Dear Amber Users;
I try to MD simulation with non-standard residue in amber11. I construct
molecule by using molecule drawing tool and gave it to gaussian to optimize
and calculate esp charges. Later, using antechamber I convert .log file
from gaussian to mol2 file with esp charges. Then run parmchk program to
make frcmod file. In this frcmod file there are several lines contains
"ATTN, need revision". How can add this parameters to this file? What will
happen, if I leave them as they are and start MD?
Thank you for your attention
seckin
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Received on Wed May 08 2013 - 03:30:02 PDT
