AMBER Archive (2009)

Subject: [AMBER] Re: question about ff

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Jun 25 2009 - 04:12:40 CDT

Quoting ". .." <m.o.m_at_live.fr>:

Dear m.o.m_at_live.fr,

Please, send your queries in the Amber mailing list & not directly to me.

> Hi,

Hi,

> I prepare my file like this for a molecule who contain C,O and H :
>
> 1- antechamber -fi gout -i file.log -fo prepi -o file.prepi -c resp

I do not use antechamber that often.

> 2- parmchk -i file.prepi -fi prepi -o file.frcmod
>
> 3- xleap -s -f $AMBERHOME/dat/leap/cmd/?????
> 4- source leaprc.??????

3- and 4- are identical

> 5- loadamberprep file.prepi

Use the mol2 file format instead of file.prepi as more convenient
See http://q4md-forcefieldtools.org/Tutorial/leap.php

> 6- loadamberparams file.frcmod
>
> 7- saveamberparm MOL file.prmtop file.inpcrd
>
> I want to create top ans crd files in GAFF and FF03 for comparing MD
> simulation result , I have some questions:
> 1- Is it necessary in all case to do step 3 and 4 or just step 3 is
> sufficient?

If you want to use 2 FF, you need to load two leaprc files one after
the other:
xleap
source leaprc.ff03
source leaprc.gaff

> 2- Is correct if i do
> for GAFF:
> xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.gaff
> source leaprc.gaff

"xleap -f leaprc.gaff" does the job

> and for FF03
>
> xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
> source leaprc.ff03

"xleap -f leaprc.ff03" does the job

> 3- Is there any effect if i do ( my molecule contain : C,O and H)
>
> xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
> source leaprc.gaff
> In this case what is my FF?
>
> Thanks in advance
>
> _________________________________________________________________
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regards, Francois

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