Hi Ming,
I think a similar post on this topic gave me "ref. Ebook: Molecular and Cellular Iron Transport By Douglas M. Templeton”, or at least that is what ended up copied as a comment line in my mdread2.f90 file. I never verified that this source contains the actual data; from the title, it would be rather odd if it did. This is why I wish I saw Dr. Case’s post earlier: I’d take his advice—which was also repeated by Dr. Simmerling to a question I had about parameters for Au—use PB instead of GB, and use the options that allow the radii to be read from the prmtop. That’s how I would do it if I had a second chance.
Best,
Matthew
> On Sep 1, 2021, at 9:21 PM, Ming Tang <m21.tang.qut.edu.au> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Hi Matthew,
>
> Thanks a lot for your quick and precious help.
>
> yes. I saw this post https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Farchive.ambermd.org%2F201111%2F0370.html&data=04%7C01%7C%7Ce23620d5f74e4984f16c08d96db01b84%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637661425405539869%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=V2RmhWaPQQ%2FpJR2UsfoXYmDBhIFiwo57QPraoKwpANQ%3D&reserved=0
> it says mdread.f, but I failed to find it. It found the mdread2.F90 file, but have no idea about how to get the values for atom I. Do you know where is the below "0.78" for FE from in the second post? Thanks.
>
> else if (atype(1:1) == 'FE' .or. atype(1:1) == 'Fe') then
> x(l165-1+i) = 0.78d0 + 1.4d0
> x(l170-1+i) = 0.00000d0
> x(l175-1+i) = -0.00000d0
> x(l180-1+i) = -0.00000d0
> x(l185-1+i) = 0.00000d0
>
> else if (atype(1:1) == 'FE' .or. atype(1:1) == 'Fe') then
> x(l165-1+i) = 0.78d0 + 1.4d0
> ________________________________
> From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
> Sent: Thursday, 2 September 2021 10:17 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Does AmberTools21 have parameters for I atom?
>
> Hi Ming,
>
> I had a similar issue recently with Fe not being recognized by MMGBSA. Please check out the relevant previous ListServe posts given below. I actually wish I found the first one by Dr. Case when I was dealing with this issue.
>
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>
> As indicated in the second of these posts, you can see what atoms are defined for MMGBSA by inspecting the mdread2.f90 source file in the AmberTools directory. You can also add parameters there, assuming you've obtained them in some respectable way. Note that the second post speaks of a “mdread” file, but since then, my understanding is that the name changed to mdread2.
>
> I hope these comments help.
>
> Best,
> Matthew
>
>
>> On Sep 1, 2021, at 8:05 PM, Ming Tang <m21.tang.qut.edu.au> wrote:
>>
>> *Message sent from a system outside of UConn.*
>>
>>
>> Dear developers,
>>
>> I came across the below problem when using mmpbsa.py in AmberTools19
>> bad atom type: i
>>
>> Does AmberTools21 handle "I" atom?
>>
>> Thanks,
>> Ming
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Received on Wed Sep 01 2021 - 20:00:02 PDT
