Oh my God,i face with wall at beginning as a BEGINNER ;)
I really appreciate you ,sir, for answering my questions patiently,I WILL BACK
soon ;)
With regards
Rose
Sent from my iPhone
> On Oct 19, 2017, at 1:14, Alex wrote:
>
> No, what I am saying is that you need to meticulously modif
No, what I am saying is that you need to meticulously modify the amber99
forcefield (if that is indeed suitable) to represent your nanosheet. The
charges have to come from appropriate sources, whether it's your Gaussian
or whatever. This will fix all forcefield-related errors you are
encountering.
On 10/18/17 5:14 PM, Rose wrote:
Oh,you mean that i should make My sheet then just optimize it(with out putting
charge) and then convert it to .pdb file and use it in MD as an input? I have
checked the literature the suitable FF was amber99.
What Alex is saying is that none of the force fie
When I use amber99 FF i face error which says: residue NA is not identified in
force field database!
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Oh,you mean that i should make My sheet then just optimize it(with out putting
charge) and then convert it to .pdb file and use it in MD as an input? I have
checked the literature the suitable FF was amber99.
Different question;) , what is the difference between using vaccum gap (that
Will be im
Hi Rose,
It sounds like a lot of things packed in a very short message, so let me
try to clarify a few points:
1. Gromacs is not DFT, it is particle-based. You simulated your nanosheet
in Gaussian and it is my understanding that you used CHELPG to obtain the
partial atomic charges.
2. Those char
first thank you for your attntion, i made ZnS nanosheet with VNL
software,it has 33 atoms,i choosed vaccum gap,then i optimized and charged
it with gaussian03,the amino acid is threonin,for the first time i want to
study the interaction of these two structures, i am not even sure that my
nano sheet
first thank you for your attntion, i made ZnS nanosheet with VNL
software,it has 33 atoms,i choosed vaccum gap,then i optimized and charged
it with gaussian03,the amino acid is threonin,for the first time i want to
study the interaction of these two structures, i am not even sure that my
nano sheet
Hi,
That would probably depend on the nanosheet material, the particular
amino acid, the solvent & ionic strength, temperature, etc, etc. But no,
there is no tutorial and yes, a "nanosheet" can be viewed as a ligand. :)
I don't know if this helps, but could you please first give us an idea
o
Hi
I am a beginner user of GROMACS, i want to simulate the interaction of nano
sheet with amino acid ,but i dont know what should do, how should i behave
with these structures ? is there any tutoroial for interaction of nano
sheet and amino acids?
is it like protein-ligand tutorial in GROMACS tuto
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