Dear David:
>The mass needs to be the correct mass, and vdW parameters can probably be
>estimated from the difference between S and Se. (Have you done the literature
>search that I suggested? There are several force fields available that cover
>the entire periodic table.) Unless you are using GB, dummy values can be
>given for those.
I have adopted your suggestion as following:
Step1: using antechamber to create a library for C6H5IS, in this step, I got the SeON.mol2 file,
and then I hand-edit this file to move S back to Se (both atom and atom type) as following:
old: 1 S 2.7480 5.6950 7.0770 ss 1 SEO 0.000000
new: 1 SE 2.7480 5.6950 7.0770 se 1 SEO 0.000000
Step2: using parmchk (not parmchk2) to creat the SeON.frcmod file. In this file there are some
"ATTN, need revision" terms. Then manunal change the MASS flag (Se mass )and NONBOND flag
parameters. It's NONBOND flag means vdW parameters? How to estimate the vdW parameters of
Se from S. The follwoing is vdW parameters for S, How about Se.
s 1.9825 0.2824
The vdW parameters will have a great influence on our MD results?
Step3 : After step1 and step2, I use tleap to generate SeON.prmtop and SeON.incrad files. In this case,
whether the SeON.prmtop is reliable for QM (or QM/MM, other solvent for MM) MD simulation.
I don't know where I have understanding your suggestions? Important files are presented in attachment.
Sorry, I still cannot understanding this sentence: "There are several force fields available that cover the entire periodic table"
I am purpose to write a automatic program to generate inputfile for QM/MM MD dimulation input files for different systems which contain
some atoms without GAFF fore filed parameteres. So I need your more suggestions, thanks very much.
Best wishes!
At 2017-03-16 20:54:26, "David Case" <david.case.rutgers.edu> wrote:
>On Thu, Mar 16, 2017, 杨满意 wrote:
>>
>> Substituting sulfur for selenium and then hand-edit the files to
>> move S back to Se
>
>> Maybe this is a good solutions for this systems, but I still have a question:
>> As described in AMBER 2016 Manual (Page 145):"QM/MM calculations
>> without link atoms require mass, charges, van der Waals and GB radii
>> in the prmtop
>> file. All bonds, angles, and dihedrals parameters involving QM atoms are
>> neglected. In the case of electrostatic embedding the charges are also
>> neglected."
>> Is this sentence means that mass, van der Waals and GB radii are
>> requried for both QM and MM regions?
>
>Yes.
>
>> If so, "hand-edit the files to move S back to Se" should change the
>> mass, van der Waals and GB radii of S back to Se. Where can I get these
>> correct parameters.
>
>The mass needs to be the correct mass, and vdW parameters can probably be
>estimated from the difference between S and Se. (Have you done the literature
>search that I suggested? There are several force fields available that cover
>the entire periodic table.) Unless you are using GB, dummy values can be
>given for those.
>
>...good luck...dac
>
>
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- application/octet-stream attachment: SeON.mol2
- application/octet-stream attachment: SeON.pdb
- application/octet-stream attachment: tleap.in
Received on Fri Mar 17 2017 - 06:00:05 PDT
