Thanks for your patient instructions!!!Now I know it.So,if I want to directly adjust the unbond parameters in the parm10.dat(of course,adding another frcmod file is better),should I do like this?
First,remove the CB from the set of equivalencces like this
C* CA CC CD CK CM CN CQ CR CV CW CY CZ CP CS
And then, add the new unbond parameter in the MOD4 section such as
" CB 1.9080 0.0860"
Thanks so much!!!
----- 原始邮件 -----
发件人: "David A Case" <dacase.chem.rutgers.edu>
收件人: "amber" <amber.ambermd.org>
发送时间: 星期五, 2021年 7 月 30日 下午 8:52:42
主题: Re: [AMBER] questions about unbond parameters
On Fri, Jul 30, 2021, 李政新 wrote:
>For examole,when I tried to run simulations for the r(ApA) systems
>using the leaprc.RNA.OL3.The leaprc.RNA.OL3 loads the parm10.dat and
>RNA.lib.There are C6 atoms in the r(ApA) systems,and the RNA.lib says that
>" "C6" "CA" 0 1 131072 18 6 0.70090",which means the corresponding atom
>types for the C6 atom is CA.But in the parm10.dat,when I try to find the
>unbond epsilon and sigamma parameter for CA atom,I can not find it(neither
>for C6).Therefore,I want to know where is the LJ parameters for the C6(or
>CA)in the simulations.Thanks a lot.
Ah...now I see. Right above the "MOD4" section is parm10.dat, there are set
of equivalences:
N NA N2 N* NC NB NT NY
C* CA CB CC CD CK CM CN CQ CR CV CW CY CZ CP CS
This means that all of the shown nitrogen parameters are the same as "N",
and the listed carbon parameters are the same as "C*". So, for CA, look in
the MOD4 section for "C*".
....dac
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Received on Fri Jul 30 2021 - 18:30:03 PDT
