Dear David,
Thank you very much for your reply quickly.
Regarding the equivalent angle, I understood and will check it with parmed.
The deviation is 6-7 degrees as average (123).
and thank you also for confirmation,
>Finally, we don't know exactly how you created the prmtop file: it's
hard to understand what you mean by "replace directly from AM1-BCC to
CNDO". It would be more helpful if you show the exact commands that
were used to create your system.
I just change the atomic charges of zwitterionic glycine manually in "wordpad" without any command for mol2 file.
I have replaced (delete and type) the charge values from AM1-BCC to CNDO in the file. Because it is not big file.
and then perform "parmchk" for it.
frcmod file is as follows:
>remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
c3-o -c -o 1.1 180.0 2.0 General improper torsional angle (1 general atom type)
NONBON
Finally, I used the "tLEaP" for assignment of force field parameters from GAFF (not GAFF2).
The file name replaced from "SUS" to "ZG-CNDO" and codes were used as same as in the tutorial linked before.
Shoud I follow other way to change the atomic charge from AM1-BCC to which listed in the literature?
Thank you very much for your time and in advance.
best regards,
Akira
________________________________
$B:9=P?M(B: David A Case <david.case.rutgers.edu>
$BAw?.F|;~(B: 2018$BG/(B11$B7n(B12$BF|(B 22:36
$B08.h(B: AMBER Mailing List
$B7oL>(B: Re: [AMBER] Preparation of force field of zwitterion glycine molecule
On Sun, Nov 11, 2018, euq1702 wrote:
>
>I was wondering if someone could help me about the procedure of creating
>forcefield of glycine zwitterion for my case.
>But I am not sure whether the following procedure is correct or
>not. Because I at least found that O-C-O angle is not equivalated to
>130.25 (degree) even if it is in the diluted situation of glycine water
>solution.
Two starting points: use parmed to see what the parameters are for your
CO2 group, with the printAngles command. You should see that the types
are c and o, and the equilibrium angle should be 130.25. If that is not
the case, something went wrong with the antechamber build.
You don't say what (average or minimized) angle you actually got. Since
atoms are subject to many forces, the average angle may deviate from the
target (130.25) for just the angle term itself. Relatively small
deviations are probably to be expected (although I have never studied
this particular functional group's geometry).
Finally, we don't know exactly how you created the prmtop file: it's
hard to understand what you mean by "replace directly from AM1-BCC to
CNDO". It would be more helpful if you show the exact commands that
were used to create your system.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
AMBER -- AMBER Mailing List<
http://lists.ambermd.org/mailman/listinfo/amber>
lists.ambermd.org
AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. It is designed to provide a forum for users of the AMBER Molecular Dynamics and related software to ask questions related to AMBER and Molecular Dynamics Simulations in general.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 12 2018 - 06:30:03 PST
