AMBER Archive (2008)

Subject: AMBER: AddIons approach

From: parul sharma (sharmaparul7373_at_gmail.com)
Date: Fri Oct 10 2008 - 06:13:51 CDT

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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