Re: [ESPResSo-users] protein self-aggregation, directional lennard jonnes

[Tristan Bereau]

Hi Sarah,

No, there's no user guide for the code. The easiest is probably to
famililarize yourself by running some of the example scripts.

As far as your questions go:
1) that's not supported by the code as it is. You may want to look at
the file src/espresso/espresso.tcl that calls the integrator. You
could add a routine before to fix some of the amino acids. To do this,
have a look at the ESPResSo manual ("part" command).
2) Hmmm that can be a fairly tedious exercise. I'd look in the same
file, as you'll want to combine vmd with the "integrate" command of
ESPResSo. But I'm not an expert on vmd online.
3) Any simulation from peptideB will output a file observables.dat.
It'll provide a time series of the potential energy.

Best,
Tristan

On Mon, Feb 4, 2013 at 2:51 PM, sarah mohamadinegad <address@hidden> wrote:
> Dear Tristan,
>
> Sorry for interrupting you again,
> Is there any user guide for peptideB?
>
> I have many question about how to change some parts of it's code to become
> suitable for my system.
> For example:
> 1) I need to fix position of one amino acid in my peptide.
> 2) How and where can I change the code to see the vmd display online,
> 3) How can I extract the energy of the system to see whether it reaches an
> equilibrium state or not?
>
> If there is any user guide, I would be grateful if you would refer it.
> Thanks in advance,
> Sarah
>
>
>
>
>
> ________________________________
> From: Tristan Bereau <address@hidden>
> To: sarah mohamadinegad <address@hidden>
> Cc: "address@hidden" <address@hidden>
> Sent: Monday, February 4, 2013 12:39 PM
>
> Subject: Re: [ESPResSo-users] protein self-aggregation, directional lennard
> jonnes
>
> Dear Sarah,
>
> No, your ".bashrc" will be in your home directory ("~/"). It's a
> hidden file (as all files that start with a "."), but you can list it
> using the command "ls -a" in your HOME directory. Just Google for
> environment variables and bash if you're lost.
>
> Best,
> Tristan
>
> On Mon, Feb 4, 2013 at 9:58 AM, sarah mohamadinegad <address@hidden>
> wrote:
>> Dear Tristan
>>
>> Sorry I am not familiar with using bash. I have two file named
>> "dot.bashrc"
>> located in (/usr/share/base-files) and
>> (/usr/share/doc/adduser/examples/adduser.local.conf.examples/skel). Do you
>> mean I should place the command:
>>
>> export PEPTIDEB_DIR=MyPath/peptideB
>>
>> in both of these files or one of them or none?
>>
>> Kinds,
>> Sarah
>>
>>
>>
>>
>>
>> ________________________________
>> From: Tristan Bereau <address@hidden>
>> To: sarah mohamadinegad <address@hidden>
>> Cc: "address@hidden" <address@hidden>
>> Sent: Monday, February 4, 2013 11:47 AM
>>
>> Subject: Re: [ESPResSo-users] protein self-aggregation, directional
>> lennard
>> jonnes
>>
>> Dear Sarah,
>>
>> You need to set the PEPTIDEB_DIR environment variable to point to the
>> peptideB directory in your system. If, say, you use bash and have
>> saved the package in ~/peptideB, call the command:
>>
>> export PEPTIDEB_DIR=~/peptideB
>>
>> you can then check that the environment variable was stored correctly
>> by invoking:
>>
>> echo $PEPTIDEB_DIR
>>
>> making sure that it returns the directory of the package. Rather than
>> typing the first command every time you open a terminal, you can
>> automate it by saving it in your ~/.bashrc file.
>>
>> (If you're using tcsh, have a look on the Internet on how to set
>> environment variable for that environment.)
>>
>> Best,
>> Tristan
>>
>> On Mon, Feb 4, 2013 at 9:11 AM, sarah mohamadinegad <address@hidden>
>> wrote:
>>> Dear Tristan
>>> I hope I can cc it this time, the last time I tried to cc my e-mail but I
>>> couldn't. Sorry!
>>>
>>> Very good news,
>>> So the point is that *relative* PID is important not the PID itself!
>>> Thanks
>>> Tristan.
>>>
>>> I have one more question.
>>> As you referred me to peptideB, I take a look and find it exactly what I
>>> need. But the installation guide is not clear enough to me. When I want
>>> to
>>> run one of your sample code "peptide.tcl", using this command:
>>>
>>> Espresso peptidebuilder.tcl peptide.tcl -espresso
>>>
>>> I faced to an error:
>>>
>>> Error. Can't find the PEPTIDEB_DIR environment variable.
>>>
>>> I know the mistake is with
>>>
>>> export PEPTIDEB_DIR=path/peptideB
>>>
>>> but I don't know exactly how and maybe where to fix it! Would you please
>>> help me with this or refer me to a more detailed installation guide?
>>>
>>> Thanks in advance,
>>> Sarah
>>>
>>>
>>>
>>>
>>>
>>>
>>> ________________________________
>>> From: Tristan Bereau <address@hidden>
>>> To: sarah mohamadinegad <address@hidden>
>>> Cc: "address@hidden" <address@hidden>
>>> Sent: Monday, February 4, 2013 11:19 AM
>>>
>>> Subject: Re: [ESPResSo-users] protein self-aggregation, directional
>>> lennard
>>> jonnes
>>>
>>> Dear Sarah,
>>>
>>> (I'm cc-ing this to the mailing list.)
>>>
>>> The interaction only needs to be set once for a pair of atom types, so
>>> there would only be one call to that command. The last 4 numbers in
>>> the 'inter' command refer to the *relative* position of neighboring
>>> atoms along the backbone chain. They allow to define the angles for
>>> the directionality of the interaction. Here's an example from the code
>>> I referred to in my last email:
>>>
>>> inter 1 2 lj-angle $eps $sigma $cut 1 -1 1 -2
>>>
>>> that describes an interaction between types 1 (i.e., N) and 2 (i.e.,
>>> C), where the direction of the amide group is given by the three atoms
>>> [N-1] N and [N+1] (consecutive along the chain), and the direction of
>>> the carbonyl group by [C-2] C and [C+1] (thus the "-2" at the end of
>>> the command. All in all, the four numbers you need to type in at the
>>> end of the command depend on the arrangement of beads (i.e., PIDs in
>>> ESPResSo) you use to create your backbone chain.
>>>
>>> Best,
>>> Tristan
>>>
>>> On Mon, Feb 4, 2013 at 7:22 AM, sarah mohamadinegad <address@hidden>
>>> wrote:
>>>> Dear Tristan,
>>>>
>>>> Thanks for your kind answer.
>>>>
>>>> Maybe describing my trouble using an example will help:
>>>>
>>>> Suppose a 200aa protein and I assign type=1 to all my C atoms and type=2
>>>> to
>>>> all N atoms. Now I need to have a hydrogen bond between a C atom with
>>>> pid
>>>> 15
>>>> and N atom with pid 148, (type=1,pid=15 -> type=2,pid=148), So using
>>>> directional LJ, I write
>>>>
>>>> inter 1 2 lj-angle $eps $sigma $cut 14 16 147 149
>>>>
>>>> Just here I have a question! this line set an interaction between all C
>>>> atoms(type=1) and all N atoms(type=2) present in my box or only my
>>>> desired
>>>> atoms?
>>>>
>>>> If I want to set hydrogen bond between all C atoms and all N atoms, what
>>>> should I write in place of the four last pids (14 16 147 149)?
>>>>
>>>> Thanks in advance,
>>>> Sarah
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ________________________________
>>>> From: Tristan Bereau <address@hidden>
>>>> To: sarah mohamadinegad <address@hidden>
>>>> Cc: "address@hidden" <address@hidden>
>>>> Sent: Sunday, February 3, 2013 6:04 PM
>>>> Subject: Re: [ESPResSo-users] protein self-aggregation, directional
>>>> lennard
>>>> jonnes
>>>>
>>>> Dear Sarah,
>>>>
>>>> How you want to model a system ultimately depends on what you want to
>>>> recreate. However, atom types for protein backbones are generally
>>>> residue-independent, i.e., one set of parameters irrespective of the
>>>> residue. The interaction potential you refer to was used in this paper
>>>> to model CG peptides:
>>>>
>>>> http://jcp.aip.org/resource/1/jcpsa6/v130/i23/p235106_s1
>>>>
>>>> This model did use one atom type for the C atoms and another one for
>>>> the N atoms. See the following link for an ESPResSo implementation of
>>>> the CG model:
>>>>
>>>> https://github.com/tbereau/peptideB
>>>>
>>>> Best,
>>>> Tristan
>>>>
>>>> On Sun, Feb 3, 2013 at 2:59 PM, sarah mohamadinegad <address@hidden>
>>>> wrote:
>>>>> Dear users and developers,
>>>>>
>>>>> I am going to model a protein (almost large >200 aa) self-aggregation
>>>>> by
>>>>> using ESPResSo. To set hydrogen bond between amino acids of protein, I
>>>>> am
>>>>> going to use directional lennard jonnes (lj-angle).
>>>>>
>>>>> As I should consider hydrogen bond between N-H group of every amino
>>>>> acid
>>>>> with C-O group of other amino acids, do I have to assign different
>>>>> types
>>>>> to
>>>>> N and C groups of different amino acids?
>>>>> For example:
>>>>> aa1  : N(type = 1) C(type = 2)
>>>>> aa2  : N(type = 3) C(type = 4)
>>>>> aa3  : N(type = 5) C(type = 6)
>>>>> aa4  : N(type = 7) C(type = 8)
>>>>> aa5  : N(type = 9) C(type = 10)
>>>>> .
>>>>> .
>>>>> .
>>>>> aa200: N(type = 399) C(type = 400)
>>>>>
>>>>> I would be happy if I can assign only one type (for example 1) to all
>>>>> of
>>>>> my
>>>>> N atoms and another one (for example 2) to all my C atoms, Is it
>>>>> possible
>>>>> for the case of my problem?
>>>>>
>>>>> Thanks in advance for your help,
>>>>> Sarah
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>