Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

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

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

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.

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

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

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

When I use amber99 FF i face error which says: residue NA is not identified in force field database! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

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

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

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

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

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

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

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

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

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