Thanks a lot. I will search.
I have done with REDtools too, but with the same result.
Thanks for your help
Regards
El abr 12, 2015 6:06 PM, "Bill Ross" <ross.cgl.ucsf.edu> escribió:
> Hi Carlos,
>
> Note the 0's in Nonbon. You need to read the literature to come up with
> real parameters. Charged particles without vdw cause problrms.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: Carlos Romero <
> carlos.rom.74he.gmail.com> </div><div>Date:04/12/2015 12:05 PM
> (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org>
> </div><div>Subject: Re: [AMBER] error in minimization </div><div>
> </div>Hi dear Bill. Thanks for your interest.
>
> The calcium.frcmod is:
>
> carlos.carlos-HP-G42-Notebook-PC:~/amber14/bin$ cat ioncalcio.frcmod
> remark goes here
> MASS
> Co2+ 0.000 0.000 ATTN, need revision
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
>
> NONBON
> Co2+ 0.0000 0.0000 ATTN, need revision
>
>
>
> thanks again
>
> Regards
>
> 2015-04-12 11:53 GMT-05:00 Bill Ross <ross.cgl.ucsf.edu>:
>
> > Hi Carlos,
> >
> > What atom type is your ion?
> > Can you show me the vdw parameters for it from your frcmod?
> >
> > Bill
> >
> > <div>-------- Original message --------</div><div>From: Carlos Romero <
> > carlos.rom.74he.gmail.com> </div><div>Date:04/11/2015 10:25 PM
> > (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org>
> > </div><div>Subject: Re: [AMBER] error in minimization </div><div>
> > </div>Hi dear Bill.
> >
> > I used the following procedure:
> >
> > xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB
> >
> > > edit CO
> > > edit selected atoms
> > > save & quit
> > > savemol2 CO calcium.mol2 1
> > > quit
> >
> > parmchk -i calcium.mol2 -f mol2 -o calcium.frcmod
> >
> > xleap -s -f $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff99SB
> >
> > ( i used ff99SB because ff14SB gave me many errors)
> > > cal = loadmol2 calcium.mol2
> > > loadamberparams calcium.frcmod
> > > p2y = loadpdb p2y.pdb
> > > addions p2y CO 16 Cl- 32
> > > solvatebox TIP3PBOX 8.0
> > > saveamberparam p2y p2y_ion_wat.prmtop p2y_ion_wat.inpcrd
> > > quit
> >
> > The min.in
> >
> > &cntrl
> > imin = 1
> > maxcyc = 2500
> > ncyc = 1000
> > ntb = 1
> > ntr = 0
> > cut =12
> > /
> >
> > These are the parameters I used
> >
> > Thanks in advance
> >
> > Regards
> > El abr 11, 2015 11:04 PM, "Bill Ross" <ross.cgl.ucsf.edu> escribió:
> >
> > > What vdw parameters do you use for Ca?
> > >
> > > Bill
> > >
> > > <div>-------- Original message --------</div><div>From: Carlos Romero <
> > > carlos.rom.74he.gmail.com> </div><div>Date:04/11/2015 1:55 PM
> > > (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org>
> > > </div><div>Subject: [AMBER] error in minimization </div><div>
> > > </div>Hi dear Amber Users,
> > >
> > > I am trying to simulate a proteín in presence of ions.
> > >
> > > When I use Cl- Na+ and K+, which are default in AMBER11, minimization
> and
> > > MD run withput problems, but when I use Calcium or lactate i get the
> > advice
> > > :
> > > RESTARTED DUE TO LINMIN FAILURE. in file.out, and in the terminal the
> > next
> > > mesaage
> > >
> > > Program received signal SIGSEGV: Segmentation fault - invalid memory
> > > reference.
> > >
> > > Backtrace for this error:
> > > #0 0xB7369163
> > > #1 0xB7369800
> > > #2 0xB77353FF
> > > #3 0x811111E in nb_adjust_
> > > #4 0x8112CDA in ewald_force_
> > > #5 0x827E724 in force_
> > > #6 0x80C277A in runmin_
> > > #7 0x80B1077 in sander_
> > > #8 0x80AA74F in MAIN__ at multisander.F90:?
> > > Violación de segmento (`core' generado)
> > >
> > >
> > > for Calcium ion I download Ambertools14 and save parameters
> > (calcium.frcmod
> > > and calcium.mol2), and for lactate I used RED-tools.
> > >
> > > Does somebody could help me please.
> > >
> > > I give thanks in advance.
> > >
> > > Regards
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Received on Sun Apr 12 2015 - 17:00:02 PDT
