Re: [AMBER] Regarding Leap

From: Charu Sharma (JRF) <"Charu>
Date: Wed, 17 Oct 2018 17:00:14 +0530

Respected sir,
 i have a doubt in this command can you please clarify this? what actuality
is the mistake i am doing

On Sun, Oct 14, 2018 at 1:33 PM Elvis Martis <elvis.martis.bcp.edu.in>
wrote:

> Hi,
> The command you used to run the SANDER job, you have used "-c" flag twice,
> hence, the error of unknown flag.
> And second, please ensure that "01_min.in" file is in the working
> directory. The error indicates it's missing or not readable.
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: Charu Sharma (JRF) <charu.sharma.lnmiit.ac.in>
> Sent: 13 October 2018 16:16
> To: amber.ambermd.org
> Subject: Re: [AMBER] Regarding Leap
>
> Hello sir,
> I am sending you the screen shot this [problem is showing by running all
> commands
>
> On Sat, Oct 13, 2018 at 1:04 PM Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > HI
> > Can you send the exact command you used, the input file and the error
> > message?
> >
> > Best Regards
> > Elvis Martis
> > Mumbai, INDIA.
> >
> > ________________________________________
> > From: Charu Sharma (JRF) <charu.sharma.lnmiit.ac.in>
> > Sent: 13 October 2018 11:28
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] Regarding Leap
> >
> > 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
> > > >
> > > _______________________________________________
> > > 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
> > >
> > _______________________________________________
> > 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
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Wed Oct 17 2018 - 05:00:01 PDT
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