AMBER Archive (2009)

Subject: [AMBER] Re: Fw:How to creat .frcmod file

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Mar 05 2009 - 00:22:56 CST

Hi Nancy,

Please, ask your next questions in the Amber mailing list...

> May I have a question ? I wonder how to creat a .prcmod file to
> check if there are missing parameters .

A frcmod file ? you mean ?

- using either the way of Antechamber for the General Amber Force
Field to do it automatically
- or manually adding missing parameters for other force fields
(capital letters for FF atom types) in your own frcmod file (to decide
what you take as FF parameters)
See for instance $AMBERHOME/dat/leap/parm/*
                                           frcmod.ff03

> Indeed ,I have modified the type of C atom and set up .lib file for
> the unit,for my pdb file is not standard residue file ,it is about
> carbon nanotubes .After set order: loadoff nan.lib, check NAN
> (NAN=loadpdb nanotube.pdb),saveamberparm NAN NAN_vac.top NAN
> _vac.inpcrd, the screen showed as Screenshot.png.Can I ignore it ?

You need to understand what LEaP tells you:
Warning, checking and building are information, so they are ok.
ERROR is ... an error and has to be corrected.

> If not ,need I creat a .frcmod file?

In the present case, you generated the prmtop/prmcrd files for NAN.
This means you do not need a frcmod file: LEaP generates the
prmtop/prmcrd files only if no FF parameter is missing.

> I have tried antechamber,but failed. What should I do? Can you give
> me some advice?

What do you want to do with Antechamber ?
Create a frcmod ? This will work for organic molecules (with a limit
for the molecule size I guess).

"I have tried antechamber,but failed". What failed ?
You cannot get help if you do not describe the error messages you got.

regards, Francois

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