what does the leap.log file say?
On Fri, Oct 10, 2008 at 7:13 AM, parul sharma <sharmaparul7373.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
>
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Received on Sun Oct 12 2008 - 05:12:21 PDT
