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

2017-10-18 Thread Roja 
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 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. In order to learn about Gromacs forcefield format and how to
> do the editing, please consult the official Gromacs documentation. This
> really needs to be done before you start doing the xyz>pdb conversions, etc.
> 
> The "vacuum gap" is a moot point for MD simulations, especially ones
> involving solvent. Please understand the differences between DFT and
> particle-based simulations. You can put your nanosheet in a bunch of
> different boxes of appropriate size. This forum isn't the right place for
> asking this, I am only replying, because I have experience with using
> Gromacs for things it was never intended. :)
> 
> Best of luck!
> 
> Alex
> 
>> On Wed, Oct 18, 2017 at 3:14 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.
>> Different question;) , what is the difference between using vaccum gap
>> (that Will be implemented in structure.xyz file) and using smaller box
>> with periodic boundry condition(with out using vaccum gap),are they related
>> to each other at all?!!!
>> Sorry for these childish questions,but I really get confused.
>> 
>> With regards
>> Roja
>> 
>> 
>>> On Oct 19, 2017, at 0:08, Alex  wrote:
>>> 
>>> 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 charges in general are not compatible with most MD forcefields
>>> implemented in Gromacs. If I remember correctly, AMBER is the closest to
>>> using CHELPG charges. So, my point is that you need to choose the MD
>>> forcefield properly and set the charges (all non-bonded parameters,
>> really)
>>> accordingly. The same goes for the bonded parameters to represent the
>>> nanomechanical properties of the sheet. This is beyond the scope of this
>>> discussion, as you definitely need to do a thorough literature search and
>>> see what forcefield is appropriate.
>>> 
>>> 3. You ask if your nanosheet is "suitable." Any structure is "suitable"
>> in
>>> principle, as long as the interactions are set properly.
>>> 
>>> It is hard to give any advice beyond that. Simulation of "custom"
>>> structures is a lot of effort. If your system of interest is small, an
>>> alternative to all of this could be DFTMD simulations using CP2K package.
>>> 
>>> Alex
>>> 
 On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani 
>> wrote:
 
 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 is suitable for this simulation or not,but for the as a
 beginning i prfeer to test it.
 
 
 
> On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:
> 
> 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
>> of
> what you're trying to do?
> 
> Alex
> 
> 
>> On 10/18/2017 1:09 PM, rose rahmani wrote:
>> 
>> 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 tutorial?
>> 
>> with regards
>> 
>> Rose
> 
> --
> 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 http://www.gromacs.org/Support/Mailing_Lists

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

2017-10-18 Thread Alex 
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. In order to learn about Gromacs forcefield format and how to
do the editing, please consult the official Gromacs documentation. This
really needs to be done before you start doing the xyz>pdb conversions, etc.

The "vacuum gap" is a moot point for MD simulations, especially ones
involving solvent. Please understand the differences between DFT and
particle-based simulations. You can put your nanosheet in a bunch of
different boxes of appropriate size. This forum isn't the right place for
asking this, I am only replying, because I have experience with using
Gromacs for things it was never intended. :)

Best of luck!

Alex

On Wed, Oct 18, 2017 at 3:14 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.
> Different question;) , what is the difference between using vaccum gap
> (that Will be implemented in structure.xyz file) and using smaller box
> with periodic boundry condition(with out using vaccum gap),are they related
> to each other at all?!!!
> Sorry for these childish questions,but I really get confused.
>
> With regards
> Roja
>
>
> > On Oct 19, 2017, at 0:08, Alex  wrote:
> >
> > 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 charges in general are not compatible with most MD forcefields
> > implemented in Gromacs. If I remember correctly, AMBER is the closest to
> > using CHELPG charges. So, my point is that you need to choose the MD
> > forcefield properly and set the charges (all non-bonded parameters,
> really)
> > accordingly. The same goes for the bonded parameters to represent the
> > nanomechanical properties of the sheet. This is beyond the scope of this
> > discussion, as you definitely need to do a thorough literature search and
> > see what forcefield is appropriate.
> >
> > 3. You ask if your nanosheet is "suitable." Any structure is "suitable"
> in
> > principle, as long as the interactions are set properly.
> >
> > It is hard to give any advice beyond that. Simulation of "custom"
> > structures is a lot of effort. If your system of interest is small, an
> > alternative to all of this could be DFTMD simulations using CP2K package.
> >
> > Alex
> >
> >> On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani 
> wrote:
> >>
> >> 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 is suitable for this simulation or not,but for the as a
> >> beginning i prfeer to test it.
> >>
> >>
> >>
> >>> On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:
> >>>
> >>> 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
> of
> >>> what you're trying to do?
> >>>
> >>> Alex
> >>>
> >>>
>  On 10/18/2017 1:09 PM, rose rahmani wrote:
> 
>  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 tutorial?
> 
>  with regards
> 
>  Rose
> >>>
> >>> --
> >>> 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 http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-requ...@gromacs.org.
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/
> >> Support/Mailing_Lists/GMX-Users_List before posting!
> >>
> >> *

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

2017-10-18 Thread Justin Lemkul 



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 fields provided with 
GROMACS has knowledge of ZnS species and you will have to provide all of 
the parameters yourself. If they exist in the literature, then you need 
to implement them. If not, you need to parametrize it from scratch - a 
very advanced and difficult task (if it can even be made to work with a 
classical, pairwise additive functional form). A PDB file without a 
corresponding topology is useless.


-Justin


Different question;) , what is the difference between using vaccum gap (that 
Will be implemented in structure.xyz file) and using smaller box with periodic 
boundry condition(with out using vaccum gap),are they related to each other at 
all?!!!
Sorry for these childish questions,but I really get confused.

With regards
Roja



On Oct 19, 2017, at 0:08, Alex  wrote:

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 charges in general are not compatible with most MD forcefields
implemented in Gromacs. If I remember correctly, AMBER is the closest to
using CHELPG charges. So, my point is that you need to choose the MD
forcefield properly and set the charges (all non-bonded parameters, really)
accordingly. The same goes for the bonded parameters to represent the
nanomechanical properties of the sheet. This is beyond the scope of this
discussion, as you definitely need to do a thorough literature search and
see what forcefield is appropriate.

3. You ask if your nanosheet is "suitable." Any structure is "suitable" in
principle, as long as the interactions are set properly.

It is hard to give any advice beyond that. Simulation of "custom"
structures is a lot of effort. If your system of interest is small, an
alternative to all of this could be DFTMD simulations using CP2K package.

Alex


On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani  wrote:

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 is suitable for this simulation or not,but for the as a
beginning i prfeer to test it.




On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:

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 of
what you're trying to do?

Alex



On 10/18/2017 1:09 PM, rose rahmani wrote:

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 tutorial?

with regards

Rose

--
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.

--
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.

--
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

*

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

2017-10-18 Thread Rose 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

2017-10-18 Thread Rose 
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 implemented in structure.xyz file) and using smaller box with periodic 
boundry condition(with out using vaccum gap),are they related to each other at 
all?!!!
Sorry for these childish questions,but I really get confused.

With regards
Roja


> On Oct 19, 2017, at 0:08, Alex  wrote:
> 
> 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 charges in general are not compatible with most MD forcefields
> implemented in Gromacs. If I remember correctly, AMBER is the closest to
> using CHELPG charges. So, my point is that you need to choose the MD
> forcefield properly and set the charges (all non-bonded parameters, really)
> accordingly. The same goes for the bonded parameters to represent the
> nanomechanical properties of the sheet. This is beyond the scope of this
> discussion, as you definitely need to do a thorough literature search and
> see what forcefield is appropriate.
> 
> 3. You ask if your nanosheet is "suitable." Any structure is "suitable" in
> principle, as long as the interactions are set properly.
> 
> It is hard to give any advice beyond that. Simulation of "custom"
> structures is a lot of effort. If your system of interest is small, an
> alternative to all of this could be DFTMD simulations using CP2K package.
> 
> Alex
> 
>> On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani  wrote:
>> 
>> 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 is suitable for this simulation or not,but for the as a
>> beginning i prfeer to test it.
>> 
>> 
>> 
>>> On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:
>>> 
>>> 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 of
>>> what you're trying to do?
>>> 
>>> Alex
>>> 
>>> 
 On 10/18/2017 1:09 PM, rose rahmani wrote:
 
 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 tutorial?
 
 with regards
 
 Rose
>>> 
>>> --
>>> 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 http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>> --
>> 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 http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
> -- 
> 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 http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.
-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

2017-10-18 Thread Alex 
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 charges in general are not compatible with most MD forcefields
implemented in Gromacs. If I remember correctly, AMBER is the closest to
using CHELPG charges. So, my point is that you need to choose the MD
forcefield properly and set the charges (all non-bonded parameters, really)
accordingly. The same goes for the bonded parameters to represent the
nanomechanical properties of the sheet. This is beyond the scope of this
discussion, as you definitely need to do a thorough literature search and
see what forcefield is appropriate.

3. You ask if your nanosheet is "suitable." Any structure is "suitable" in
principle, as long as the interactions are set properly.

It is hard to give any advice beyond that. Simulation of "custom"
structures is a lot of effort. If your system of interest is small, an
alternative to all of this could be DFTMD simulations using CP2K package.

Alex

On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani  wrote:

> 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 is suitable for this simulation or not,but for the as a
> beginning i prfeer to test it.
>
>
>
> On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:
>
> > 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 of
> > what you're trying to do?
> >
> > Alex
> >
> >
> > On 10/18/2017 1:09 PM, rose rahmani wrote:
> >
> >> 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 tutorial?
> >>
> >> with regards
> >>
> >> Rose
> >>
> >
> > --
> > 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 http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> 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 http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

2017-10-18 Thread rose rahmani 
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 is suitable for this simulation or not,but as a beginning i
prefer to test it

On Wed, Oct 18, 2017 at 11:20 PM, rose rahmani 
wrote:

> 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 is suitable for this simulation or not,but for the as a
> beginning i prfeer to test it.
>
>
>
> On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:
>
>> 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 of
>> what you're trying to do?
>>
>> Alex
>>
>>
>> On 10/18/2017 1:09 PM, rose rahmani wrote:
>>
>>> 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 tutorial?
>>>
>>> with regards
>>>
>>> Rose
>>>
>>
>> --
>> 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 http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

2017-10-18 Thread rose rahmani 
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 is suitable for this simulation or not,but for the as a
beginning i prfeer to test it.



On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:

> 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 of
> what you're trying to do?
>
> Alex
>
>
> On 10/18/2017 1:09 PM, rose rahmani wrote:
>
>> 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 tutorial?
>>
>> with regards
>>
>> Rose
>>
>
> --
> 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 http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

2017-10-18 Thread Alex 

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 
of what you're trying to do?


Alex

On 10/18/2017 1:09 PM, rose rahmani wrote:

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 tutorial?

with regards

Rose


--
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.