Hello sir,
I would like to know ,i have created the AMBER MD sander input files .
While following the step of RUN AMBER MD sander ,run the minimization of
alanine dipeptide with sander but it showing error of unknown flag why ?
when i gave enter command for it .
On Wed, Oct 10, 2018 at 8:48 PM Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> HI,
> Once you have installed AMBER.
> type the following in your terminal
> source $AMBERHOME/amber.sh
> or
> source $AMBERHOME/amber.csh
> and then type
> xleap
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: Charu Sharma (JRF) <charu.sharma.lnmiit.ac.in>
> Sent: 10 October 2018 16:31
> To: amber.ambermd.org
> Subject: Re: [AMBER] Regarding Leap
>
> Hello sir,
> I want to know how to run the command of xleap in ubuntu while working in
> linux.
>
> On Tue, Oct 9, 2018 at 11:13 AM Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > Hi Charu/Karishma,
> > It is highly recommended that you read the AMBER manual (
> > http://ambermd.org/doc12/Amber18.pdf), and also, visit the amberMD web
> > page (http://ambermd.org/FileFormats.php) that has all your answers.
> > Here, you will find information on FF14SB (
> > http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00255)
> > Leaprc.ff14SB is the file to source Amber14 force field parameters.
> > FYI, from AMBER16 onwards this is "leaprc.protein.ff14SB"
> >
> > Hope this helps
> >
> > Best Regards
> > Elvis Martis
> > Mumbai, INDIA.
> >
> > ________________________________________
> > From: Charu Sharma (JRF) <charu.sharma.lnmiit.ac.in>
> > Sent: 09 October 2018 10:03
> > To: amber-subscribe.ambermd.org; Dr. Ashok Garai; AMBER.ambermd.org
> > Subject: [AMBER] Regarding Leap
> >
> > Hello everyone,
> > This is karishma , i want to know basic difference between AMBER topology
> > file extension, coordinates file extension as well as about
> Leaparc.ff14SB.
> >
> > Thanking you,
> >
> >
> > Regards
> >
> > karishma Sharma
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
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>
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Received on Fri Oct 12 2018 - 23:00:02 PDT
