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

From: sarah mohamadinegad
Subject: Re: [ESPResSo-users] protein self-aggregation, directional lennard jonnes
Date: Mon, 4 Feb 2013 00:11:16 -0800 (PST)

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,


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.


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:
> 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:
> 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

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