Dear Pengfei,
many thanks for your explanation and the advice! Will try it after coming
back from vacation.
Sincerely,
Nick
Message: 2
Date: Tue, 9 Oct 2018 19:59:30 -0400
From: Pengfei Li <ambermailpengfei.gmail.com>
Subject: Re: [AMBER] Full: Parameters for atom CE in lj_1264_pol.dat
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <333CCD7B-61EE-4A36-A5A5-5F76E8729056.gmail.com>
Content-Type: text/plain; charset=utf-8
Dear Nikolay,
The error is because in the 12-6-4 model in AMBER when two atom types share
the same VDW parameters, they should have the same polarizability parameter
as well.
The error message tells you that CI and CE have the same VDW parameters,
but their polarizability parameters are different in the lj_1264_pol.dat
file.
The polarizability of CI is 1.061 in the lj_1264_pol.dat file, so the
polarizability of CE should be 1.061 as well. So you can change the ?CE
1.352? to ?CE 1.061? and try it again.
Hope it helps,
Pengfei
> On Oct 8, 2018, at 5:29 AM, Nikolay N. Kuzmich <nnkuzmich.gmail.com>
wrote:
>
> Dear Amber users,
>
> sorry, I accidently sent unfinished letter previously.
>
> I was trying to add 12-6-4 parameters to Na+ and Cl- ions in the system
> containing DNA (bsc1 force field).
> The result was
>
>> add12_6_4 .Na+,Cl- watermodel SPCE
> Adding Lennard-Jones C-coefficient for 12-6-4 potential. Polarizabilities
> read from [/home/nick/amber18/dat/leap/parm/lj_1264_pol.dat]. Using
default
> C4 parameters for water model [SPCE].
> ***********************************************************
> The selected metal ion is Na
> The selected metal ion is Cl
> Action add12_6_4 failed
> LJ12_6_4Error: Could not find parameters for ATOM_TYPE CE
>> quit
>
> Then I decided to experiment and added vdW parameter for CE in the
> lj_1264_pol.dat:
>
> CE 1.352
> and tried again:
>
>> add12_6_4 .Na+,Cl- watermodel SPCE
> Adding Lennard-Jones C-coefficient for 12-6-4 potential. Polarizabilities
> read from [/home/nick/amber18/dat/leap/parm/lj_1264_pol.dat]. Using
default
> C4 parameters for water model [SPCE].
> ***********************************************************
> The selected metal ion is Na
> The selected metal ion is Cl
> Action add12_6_4 failed
> LJ12_6_4Error: Polarizability parameter of AMBER_ATOM_TYPE
> CI is not the same as that of AMBER_ATOM_TYPE CE but their VDW parameters
> are the same.
>
> How is it possible to solve the issue with CE parameter and polarizability
> and with adding 12-6-4 to the system? For a protein sytem it worked well.
>
> Kind regards,
> Nick
>
> Nikolay Kuzmich
> Department of Drug Safety,
> Research Institute of Influenza,
> WHO National Influenza Centre of Russia,
> 15/17 Professor Popov St.,
> Saint-Petersburg
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Oct 12 2018 - 09:00:02 PDT
