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
> _______________________________________________
> 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 Sun Apr 12 2015 - 10:00:03 PDT
