I am trying to restraint my dihedral angles in order to keep the beta
strands intact while simulating the peptide. but each time my peptide
change the beta strands to coils while simulating. Can anyone help me with
the rst files please.
On Fri, Dec 4, 2015 at 2:06 PM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
wrote:
> Dear Jason,
> my issue has been resolved.
> thank you
> and i also need your guidance for adding TIP3box ... what steps i should
> take ? have i first select forcefield after that load ligand.pdb file and
> then complex.pdb and protein.pdb files on xleap and then neutralize charges
> and after that add water ? please guide me for whole steps what should i
> have to do step by step . i'll be very thankful to you.
> Regards
>
> > Date: Thu, 3 Dec 2015 07:42:50 -0500
> > From: jason.swails.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] xleap terminal terminate
> >
> > On Thu, Dec 3, 2015 at 7:33 AM, Ayesha Kanwal <
> ayesha_comsian.hotmail.com>
> > wrote:
> >
> > > Dear amber experts,
> > > hope you all will be fine.
> > > i am working on antechamber for generating prmtop files for ligand ,
> > > complex and receptor.
> > > i had already generated ligand and complex prmtop file but for receptor
> > > when i want to save amberparam on xleap , xleap suddenly terminate and
> an
> > > error shown on the terminal as segmentation fault.
> > > any suggestion why it is happened every time only for receptor ?
> > >
> >
> > ​Segmentation fault simply says that something went wrong, and it's an
> > internal error inside tleap. It says nothing about *what* went wrong.
> As
> > far as error messages go, "Segmentation fault" is one of the least
> helpful
> > out there.
> >
> > So we would need more details -- specifically the leap commands or leap
> > script you used in addition to the input files so we can try to reproduce
> > it.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>
--
Mary Dutta
Research Scholar
Department of MBBT
Tezpur University
ph. no: 8721841782
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Received on Fri Dec 04 2015 - 02:30:04 PST
