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 - 16:30:03 PDT
