You need to define the atom type (e.g. As) of the atom named As in the
residue named ARS in the atomic_ions.lib, presumably with the As.in
script, and the mass and R*/epsilon of that type need to be on separate
lines in frcmod.ions234lm_126_spce.
If you have further questions, please show how you are handling these
elements.
Bill
On 12/15/17 6:04 AM, MinYuan wrote:
> Hi Pengfei,
>
> Thank you for your nice reply!
> I had a try, but didn't get it.
>
> 1. To create As3+ library file, I added As3+ into atomic_ions.lib via tleap -s -f As.in.
> 2. I took the parameters you gave as 12-6 LJ parameters.
> And added the Rmin/2 and epsilon into frcmod.ions234lm_126_spce file.
> 3. Added {"As3+" "As" "sp3" } into leaprc.water.spce file.
>
> 4. tleap -s -f As_leap.in > As_leap.out, ERROR occured.
> In leap.log file:
> FATAL: Atom .R<ARS 18>.A<As 1> does not have a type.
>
> How to use the two parameters in a correct way?
>
> Looking forward to receive your help.
>
> Best wishes
> Yuan Min
>> -----原始邮件-----
>> 发件人: "Pengfei Li" <ambermailpengfei.gmail.com>
>> 发送时间: 2017-12-14 00:54:52 (星期四)
>> 收件人: "AMBER Mailing List" <amber.ambermd.org>
>> 抄送:
>> 主题: Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib
>>
>> Hi Yuan,
>>
>> I have replied another email you sent to you about this issue. Hope it can solve your problem.
>>
>> Kind regards,
>> Pengfei
>>
>>> On Dec 12, 2017, at 9:11 PM, MinYuan <minyuan.mail.ustc.edu.cn> wrote:
>>>
>>> Hi,
>>>
>>> I want to simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib.
>>> Is there any way to deal with it?
>>> The tutorial here doesn't work. http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.html
>>>
>>> Looking forward to hear your help.
>>>
>>> Best wishes
>>> Yuan Min
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
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Received on Fri Dec 15 2017 - 06:30:06 PST
