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
>>>>
>>>>
>>>
>>>
>>
>>
>
>