Hi Matthew,
Thanks a lot for your quick and precious help.
yes. I saw this post
http://archive.ambermd.org/201111/0370.html
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.
https://urldefense.com/v3/__http://archive.ambermd.org/201606/0311.html__;!!NVzLfOphnbDXSw!QNksDUP1YCLZnXpxX5ZJCU5MwveF5BYLOreh341e1woB5pFdBVmV5MkOiZp2JgiR_nx1$ <
https://urldefense.com/v3/__http://archive.ambermd.org/201606/0311.html__;!!NVzLfOphnbDXSw!QNksDUP1YCLZnXpxX5ZJCU5MwveF5BYLOreh341e1woB5pFdBVmV5MkOiZp2JgiR_nx1$ >
https://urldefense.com/v3/__http://archive.ambermd.org/201303/0230.html__;!!NVzLfOphnbDXSw!QNksDUP1YCLZnXpxX5ZJCU5MwveF5BYLOreh341e1woB5pFdBVmV5MkOiZp2Jp5kwHrz$ <
https://urldefense.com/v3/__http://archive.ambermd.org/201303/0230.html__;!!NVzLfOphnbDXSw!QNksDUP1YCLZnXpxX5ZJCU5MwveF5BYLOreh341e1woB5pFdBVmV5MkOiZp2Jp5kwHrz$ >
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 - 18:30:02 PDT
