[AMBER] ions params for SPC/F water

From: Bruno Rodrigues <bbrodrigues.gmail.com>
Date: Thu, 21 Jul 2011 00:39:50 -0300

Dear All,

I'm trying to use SPC/F for water to simulate with DNA. However, I could not
find a parameter file for the ions on this force field.
The only ones available are

When I run leap with the following codes

set WAT.1 name "SPF"
set HOH.1 name "SPF"
loadoff ions08.lib #topologies for ions with the new naming

loadAmberParams frcmod.spcfw
set default FlexibleWater on

x = loadpdb 1D20.pdb
addions x Na+ 0
solvateoct x SPCFWBOX 12.0
saveamberparm x 1D20_wat_spcf.top 1D20_wat_spcf.crd

I get this message error on leap.log

> saveamberparm x 1D20_wat_spcf.top 1D20_wat_spcf.crd
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<Na+ 21>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 22>.A<Na+ 1> Could not find type: Na+

If I put one of the three ion force fields, the error vanishes, but I saw
that they have different values
for the Na+ properties, so which ion parameter should I use to correctly
simulate this force field?

Thank you in advance!

Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Wed Jul 20 2011 - 21:00:03 PDT
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