Hi Zhu,
You can find most information regarding file formats here:
https://ambermd.org/FileFormats.php
In this particular case it refers to the atom polarizability used in some
FFs.
Cheers,
El sáb., 14 nov. 2020 a las 18:38, Zhu Liang (<zliang8.uic.edu>) escribió:
> Hi everyone,
>
> I am new to Amber, and I would like to ask a question that might sounds
> silly to you.
>
> What does the second numeric column mean? I know the first column mean
> atomic mass, but I couldn’t find anything about the second.
>
> E.g. What does 0.616 mean for atom type c in the following segment?
>
> AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
> c 12.01 0.616 Sp2 C carbonyl group
> c1 12.01 0.360 Sp C
> c2 12.01 0.360 Sp2 C
> c3 12.01 0.878 Sp3 C
> ca 12.01 0.360 Sp2 C in pure aromatic systems
> cp 12.01 0.360 Head Sp2 C that connect two rings in
> biphenyl sys.
> cq 12.01 0.360 Head Sp2 C that connect two rings in
> biphenyl sys. identical to cp
> cc 12.01 0.360 Sp2 carbons in non-pure aromatic
> systems
> cd 12.01 0.360 Sp2 carbons in non-pure aromatic
> systems, identical to cc
> ce 12.01 0.360 Inner Sp2 carbons in conjugated
> systems
> cf 12.01 0.360 Inner Sp2 carbons in conjugated
> systems, identical to ce
> cg 12.01 0.360 Inner Sp carbons in conjugated systems
> ch 12.01 0.360 Inner Sp carbons in conjugated
> systems, identical to cg
> cx 12.01 0.360 Sp3 carbons in triangle systems
> cy 12.01 0.360 Sp3 carbons in square systems
> cu 12.01 0.360 Sp2 carbons in triangle systems
>
>
> Thank you very much!
>
> Zhu
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>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Sat Nov 14 2020 - 10:00:03 PST
