> 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
Is that the exact cmd line you used? If so, I doubt it would load the file.
Bll
On 4/22/16 5:39 AM, Nikolay N. Kuzmich wrote:
> 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 - 09:30:03 PDT
