Can you write steps or you have a Doing the same step as you written.
you first upload all leaprc file.
leaprc.water.opc
slovatebox
ions
saveamberparm
savepdb
In cmd( directory different type of leaprc file so you upload one by one
related to ion and water system
On Tue, Sep 12, 2017 at 9:04 PM, Jeyaram R A <ra.jeyaram.vit.ac.in> wrote:
> Dear Aashish,
> I am using amber 16. I am new one to amber, so that i
> follow the amber tutorial for my learning purpose. I try that the
> leaprc.water.opc as commented by you. But again it shows the same problem.
> Please send me the modified command for my work.
>
> Thank you
> with regards,
> R.A. Jeyaram
> ________________________________________
> From: Aashish Bhatt <aashish.ph16221.inst.ac.in>
> Sent: Tuesday, September 12, 2017 8:39 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Atom does not have file type -reg.
>
> Hello, Jeyaram
>
> You upload leaprc.water.opc file. so they automatically upload all file.
> if you using amber 16 the path is Software/amber16/dat/leap/cmd
>
> hopefully, file is work
>
> On Tue, Sep 12, 2017 at 7:51 PM, Jeyaram R A <ra.jeyaram.vit.ac.in> wrote:
>
> > Thank You, i forget to introduce the force field for protein. Now i use
> > protein.ff14SB. But now i have the error due to the Sodium atom. For
> this
> > case, i used loadamberparams frcmod.ionsjc_tip3p. Again it shows the same
> > error. I use the following commands in tleap
> > >source leaprc.gaff
> >
> > >source leaprc.protein.ff14SB
> >
> > >loadamberprep 1.prepin
> >
> > >loadamberprep na.prepin
> >
> > >loadamberparams 1.frc
> >
> > >loadamberparams gaff.dat
> >
> > >loadamberparams frcmod.ionsjc_tip3p
> >
> > >abc = loadpdb 2.pdb
> >
> > >addions abc Na +1
> >
> > >source leaprc.water.tip3p
> >
> > >solvatebox abc TIP3PBOX 10.0
> >
> > >saveamberparm abc 1.top 1.crd
> > I got the error message as :
> > For atom: .R<Na+ 324>.A<Na 1> Could not find vdW (or other) parameters
> for
> > type: Na
> >
> >
> > Thank You
> > with regards,
> > R. A. Jeyaram
> >
> > ________________________________________
> > From: David A Case <david.case.rutgers.edu>
> > Sent: Tuesday, September 12, 2017 4:51 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Atom does not have file type -reg.
> >
> > On Mon, Sep 11, 2017, Jeyaram R A wrote:
> > >
> > >
> > > FATAL: Atom .R<ASN 22>.A<CA 2> does not have a type.
> >
> > Did you load a protein force field? Look carefully at your tleap output.
> > One (often frustrating) feature/bug of tleap is that it will soldier
> > on even if there are errors. So (for example) if you misspelled the name
> > of the protein force field you want, tleap would print an error message,
> > but continue on, giving errors like that above.
> >
> > Of course, there are other things that could have gone wrong, but the
> > output from tleap is pretty informative, once you get some experience in
> > reading it.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > 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
Received on Tue Sep 12 2017 - 09:00:03 PDT
