Dear Bill and other Amber users,
after starting XLEaP and loading ff14SB force field parameters by
$AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB
I have specified the recommended parameters for monovalent ions in TIP3P
water (12-6-4 set) by Li, Song and Merz in the command line:
frcmod.ions1lsm_1264_tip3p
when trying to save the solvated DNA the parameter file could not be saved
again.
Thank you in advance,
Nick
------------------------------
Message: 12
Date: Wed, 20 Apr 2016 01:33:09 -0700
From: Bill Ross <ross.cgl.ucsf.edu>
Subject: Re: [AMBER] XLeap didn't save the parameter file
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <57173EC5.2050002.cgl.ucsf.edu
>
Content-Type: text/plain; charset=windows-1252; format=flowed
The solution is to figure which ion parameters to load for your model.
This looks promising:
" The 12-6 LJ nonbonded model is widely used due to its simple form and
excellent transferability. Li et al. have parameterized the 12-6 model
for more than 60 ions spanning from monovalent to tetravalent across the
periodic table.[2]
<
http://ambermd.org/tutorials/advanced/tutorial20/#ref2>[5]
<
http://ambermd.org/tutorials/advanced/tutorial20/#ref5>[6]
<
http://ambermd.org/tutorials/advanced/tutorial20/#ref6>These parameters
are available in current the AMBER force field Please check the*Amber
force fields-->Molecular mechanics force fields-->Ions*section in the
manual for more details)."
Bill
On 4/20/16 1:27 AM, Nikolay N. Kuzmich wrote:
> Dear Amber users,
>
> in course of DNA polyA-polyT decamer tutorial
> when I tried to create prmtop and inpcrd files for Na+ solvated DNA by
>
> saveamberparm dna1 polyAT_cio.prmtop polyAT_cio.inpcrd
>
> the result was:
>
> Checking Unit.
> Building topology.
> Building atom parameters.
> For atom: .R<Na+ 21>.A<Na+ 1> Could not find vdW (or other) parameters for
> type: Na+
> .........................................
> .................................and so on
> Parameter file was not saved.
>
> The forcefield was FF14SB.
>
> How one can solve this problem?..
>
> Kind regards,
> Nick
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Received on Fri Apr 22 2016 - 06:00:05 PDT
