AMBER Archive (2008)

Subject: Re: AMBER: AddIons approach

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Oct 10 2008 - 06:17:08 CDT

what does the leap.log file say?

On Fri, Oct 10, 2008 at 7:13 AM, parul sharma <sharmaparul7373_at_gmail.com> wrote:
> Dear Amber users,
>
> The problem i am facing is very strange, would be really thankful if you
> could help me out with it. I tried to add ions to my peptides in water box,
> but when i create the pdb after getting the 1000.rst file after sander
> minimization, it doesn't show any ions in it.
>
> The leaprc looks like:
>
> source leaprc.ff96
> loadAmberParams frcmod.WAT
> nmb = sequence {NGLY ASN LEU TRP ALA THR GLY HIS PHE MET NHE}
> solvateBox nmb TIP3PBOX 12
> addIons nmb Na 14 Cl 15
> saveamberparm nmb nmb.prmtop nmb.prmcrd
> quit
>
> It gave me the crd and top files and i performed sander minimization, got
> 1000.rst file, and it successfully crated the pdb too, but without ions.
> Please help me.
>
> Kind Regards
> Parul Sharma
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu