Hi Pengfei,
I read your article about 12-6-4 LJ-type nonbonded model in explict water.
It says Rmin, ε for the VDW interactions and the C4 term for the ion-induced dipole interactions.
For trivalent and tetravalent metal ions, 12-6-4 type parameters for different water model can reproduce the exp. data simualtaneously.
The parameters you provided are Rmin and ε.
If they are 12-6 type, are they HFE or IOD parameter set? How about the type of water model?
Sorry for bothering you.
Best wishes
Yuan Min
minyuan.mail.ustc.edu.cn
From: Pengfei Li
Date: 2017-12-15 23:58
To: AMBER Mailing List
Subject: Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib
Hi Yuan,
You can create an independent lib file for As3+ and load it (I personally did not encourage you to modify the original force field parameter files due to it is not easy to trace the modifications back in the future).
Here is the cmd file content:
i = createAtom AS As3+ 3.0
set i element "As"
set i position { 0 0 0 }
r = createResidue ARS
add r i
ARS = createUnit ARS
add ARS r
saveOff ARS ./ARS.lib
You can use it to create an ARS.lib file and then load it, please let me know whether it works.
Kind regards,
Pengfei
> On Dec 15, 2017, at 8:04 AM, MinYuan <minyuan.mail.ustc.edu.cn> 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 Sun Dec 17 2017 - 23:00:02 PST
