Thank you very much sir
On 25 January 2015 at 01:30, <amber-request.ambermd.org> wrote:
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> AMBER Mailing List Digest
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> Today's Topics:
>
> 1. bcl script side chain optimization using Gaussian-Reg (sailu)
> 2. Re: bcl script side chain optimization using Gaussian-Reg
> (Pengfei Li)
> 3. Re: How to save structure at every minimisation/optimization
> cycle (David A Case)
> 4. Re: unusual structure after heating. why? (Atila Petrosian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 24 Jan 2015 16:44:51 +0530
> From: sailu <sai.ktp.gmail.com>
> Subject: [AMBER] bcl script side chain optimization using Gaussian-Reg
> To: AMBER.ambermd.org
> Message-ID:
> <CAMNsKYUYgOYXXaEk9DGzFk_Tsm8pEx1=
> dydLagSSUA0KOvwPGg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello amber users,
>
> I just followed the MCPB tutorial to parameterize ZN metal of my protein.
> I have run the blc script for sidechain model and generated the gaussian
> input files for optimization. Then, how to run optimization using gaussian
> ! Any script available to run this job? Please help in this reg.
>
> Thanking you
>
>
> --
> *Sarvagalla sailu,*
> *Ph.D.scholar,*
> *Centre for Bioinformatics,*
> *School of Life Sciences,*
> *Pondicherry University**,*
> *Kalapet,*
> *Puducherry - 605014**,*
> *INDIA**.*
> *Mobile: +91-9963202788,**+91-9943923258*
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 24 Jan 2015 07:53:19 -0500
> From: Pengfei Li <ambermailpengfei.gmail.com>
> Subject: Re: [AMBER] bcl script side chain optimization using
> Gaussian-Reg
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <116D2F75-C671-4B54-8756-BC4AA20FF41B.gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Sailu,
>
> I recommend you use Gaussian 03 to do the calculation.
>
> If you have Gaussian03 installed. You can use the command is like "g03 <
> example.com > example.log file". (com file is the input file while log
> file is the output file.)
>
> Hope that helps,
> Pengfei
>
> On Jan 24, 2015, at 6:14 AM, sailu <sai.ktp.gmail.com> wrote:
>
> > Hello amber users,
> >
> > I just followed the MCPB tutorial to parameterize ZN metal of my
> protein.
> > I have run the blc script for sidechain model and generated the gaussian
> > input files for optimization. Then, how to run optimization using
> gaussian
> > ! Any script available to run this job? Please help in this reg.
> >
> > Thanking you
> >
> >
> > --
> > *Sarvagalla sailu,*
> > *Ph.D.scholar,*
> > *Centre for Bioinformatics,*
> > *School of Life Sciences,*
> > *Pondicherry University**,*
> > *Kalapet,*
> > *Puducherry - 605014**,*
> > *INDIA**.*
> > *Mobile: +91-9963202788,**+91-9943923258*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 24 Jan 2015 11:16:48 -0600
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] How to save structure at every
> minimisation/optimization cycle
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150124171648.GA1044.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Fri, Jan 23, 2015, Kshatresh Dutta Dubey wrote:
> >
> > the output verbosity? I used xmin_verbosity=1, but it gives same as
> default
> > (xmin_verbosity=0). I have used following input which runs fine.
>
> Please try xmin_verbosity=2. If you need more info, you'll probably have
> to modify the code.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 24 Jan 2015 22:44:06 +0330
> From: Atila Petrosian <atila.petrosian.gmail.com>
> Subject: Re: [AMBER] unusual structure after heating. why?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAON_0oVZ3XGqD35L+P17EV4Rr-EHtAnwWOWxMUqQbifev7L=
> 0Q.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Daniel
>
> Based on your good suggestion, I installed ambertools14. I used 'autoimage'
> command in cpptraj and my problem was solved. Now, when I mdcrd file using
> VMD, all molecules (protein + ligand + water) are inside of box.
>
> I used following commands for autoimaging:
>
> parm comp1_sol.prmtop
>
> trajin prod.mdcrd
>
> autoimage
>
> trajout autoimaged.mdcrd
>
> I calculated rmsd during trajectory,
>
> parm comp1_sol.prmtop
>
> trajin autoimaged.mdcrd
>
> rms first mass out 1.rmsd .CA,C,N
>
> Unfortunately, rmsd plot is unusual. There is a maximum in the plot and
> rmsd values are relatively high, please note the figure in the following
> link :
>
> (https://www.dropbox.com/s/m9xkh0g4rb7oovo/rmsd.png?dl=0)
>
> Note that rmsd plot before and after autoimaging is the same.
>
> Trajectory includes 10 ns (2000 frames).
>
> Is this rmsd plot normal and usual? If not, please help me to resolve this
> problem.
>
> Best wishes,
> Atila
>
>
> ------------------------------
>
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> End of AMBER Digest, Vol 1109, Issue 1
> **************************************
>
--
*Sarvagalla sailu,*
*Ph.D.scholar,*
*Centre for Bioinformatics,*
*School of Life Sciences,*
*Pondicherry University**,*
*Kalapet,*
*Puducherry - 605014**,*
*INDIA**.*
*Mobile: +91-9963202788,**+91-9943923258*
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Received on Sat Jan 24 2015 - 21:30:02 PST
