Re: [gmx-users] What is best way to get multiple chains?

2009-10-14 Thread Justin A. Lemkul



ms wrote:


Wonderful advice! (and also Justin Lemkul one). Thanks for your help. Do
you mind if I later I try to update the "multiple chains" wiki page
based on your advices?


Updates from users who have relevant experience is what continually makes the 
documentation better!  The section on "Non-identical chains" is not written as 
clearly as it could be.  I'll update it a bit soon, but anything you can add 
based on your experiences would probably be quite useful as well.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] What is best way to get multiple chains?

2009-10-14 Thread ms
Mark Abraham ha scritto:
> ms wrote:
>> Mark Abraham ha scritto:
>>> What do you want the chain identifiers for? I'm not aware of a
>>> post-pdb2gmx purpose that they might serve.
>>
>> This is where my naivety probably enters in: Analysis programs work on
>> groups. If several chains are defined, can each of these count as a
>> group? Indeed, chapter 8 doesn't explicitly say so, but... My intention
>> is to get analysis for each chain in my system. What is best practice
>> for that / where should I look in the docs?
> 
> make_ndx is the tool for generating such groups. If you read make_ndx -h
> you'll see it does indeed let you create groups based around chain IDs,
> but that'd (at least) require supplying it with a coordinate file that
> has chain IDs. You could do that, but doing the house-keeping to assign
> those IDs is tricky, and with PDB you're probably limited by 26 letters.
> make_ndx will also let you create a group according to a range of atomic
> numbers "a 1-10" or residue numbers "r 1-10". This avoids needing to
> preserve/create chain IDs. Since you only need to create index groups
> once for a given coordinate file, that's not too onerous. If you will
> have lots of simulations with different numbers of such groups then you
> might write a script to automate that... see
> http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive
> 

Wonderful advice! (and also Justin Lemkul one). Thanks for your help. Do
you mind if I later I try to update the "multiple chains" wiki page
based on your advices?

>>> If your system is N identical peptides in a solvent, then best practice
>>> for generating a complete .top is to generate one for a single peptide
>>> in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a
>>> coordinate file which contains the N peptides' coordinates followed by
>>> all the solvent (e.g. genconf - genbox). Then edit the [ molecules ]
>>> section of the original .top to match. Other solutions are possible, but
>>> require more involved use of pdb2gmx, and might indeed want chain IDs.
>>
>> Uh, thanks. Not sure to have understood all of it, but I will do my
>> homework before coming back :)
> 
> Sure. Doing some "irrelevant" tutorial material can be useful
> introductions to the workflows. Regard;ess, the learning curve can be
> steep for all computational chemistry software. Unfortunately no
> beginner these days seems to want to come in and just do
> protein-in-water :-) That makes their life hard.

Yep, unfortunately that's kinda not simply "protein-in-water". I am
trying to understand all pieces I need very slowly, step-by-step. And I
guess you will hear my cries often in this ML :)

Thanks again,

m.
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Re: [gmx-users] What is best way to get multiple chains?

2009-10-14 Thread Mark Abraham

ms wrote:

Mark Abraham ha scritto:

ms wrote:

Hi,

I am a gmx newbie, so please don't bite too much! :)

Learning gmx, I am experimenting with simulations with multiple
identical small chains. What I did was:

- I generated the peptides with pymol
- Generated a .gro with pdb2gmx

This step is "generating a molecular topology". You don't need a .gro -
it's just a regularized coordinate file produced as a side-effect.


Very much right. Thanks.


- Used editconf to create translated copies

Try genconf to do the replication. That should remove much of the manual
labour. You would still probably need to edit in the chain IDs yourself,
but that's easy work with a script or good editor.


Thanks!


- Stitching them together and creating the complete file, adjusting
numbers etc. manually

It worked well, but the chains are not recognized as *different* chains
-which could be useful. Documentation says I should use another format
like the pdb, but it is a bit sparse on the subject. I think I can use
pdb instead of gro if needed, but does this also work when creating
boxes etc.? Isn't there a way to get chain identifiers in a gro file?
What is best practice?

What do you want the chain identifiers for? I'm not aware of a
post-pdb2gmx purpose that they might serve.


This is where my naivety probably enters in: Analysis programs work on
groups. If several chains are defined, can each of these count as a
group? Indeed, chapter 8 doesn't explicitly say so, but... My intention
is to get analysis for each chain in my system. What is best practice
for that / where should I look in the docs?


make_ndx is the tool for generating such groups. If you read make_ndx -h 
you'll see it does indeed let you create groups based around chain IDs, 
but that'd (at least) require supplying it with a coordinate file that 
has chain IDs. You could do that, but doing the house-keeping to assign 
those IDs is tricky, and with PDB you're probably limited by 26 letters. 
make_ndx will also let you create a group according to a range of atomic 
numbers "a 1-10" or residue numbers "r 1-10". This avoids needing to 
preserve/create chain IDs. Since you only need to create index groups 
once for a given coordinate file, that's not too onerous. If you will 
have lots of simulations with different numbers of such groups then you 
might write a script to automate that... see 
http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive



If your system is N identical peptides in a solvent, then best practice
for generating a complete .top is to generate one for a single peptide
in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a
coordinate file which contains the N peptides' coordinates followed by
all the solvent (e.g. genconf - genbox). Then edit the [ molecules ]
section of the original .top to match. Other solutions are possible, but
require more involved use of pdb2gmx, and might indeed want chain IDs.


Uh, thanks. Not sure to have understood all of it, but I will do my
homework before coming back :)


Sure. Doing some "irrelevant" tutorial material can be useful 
introductions to the workflows. Regard;ess, the learning curve can be 
steep for all computational chemistry software. Unfortunately no 
beginner these days seems to want to come in and just do 
protein-in-water :-) That makes their life hard.


Mark
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Re: [gmx-users] What is best way to get multiple chains?

2009-10-14 Thread Justin A. Lemkul



ms wrote:

Mark Abraham ha scritto:

ms wrote:

Hi,

I am a gmx newbie, so please don't bite too much! :)

Learning gmx, I am experimenting with simulations with multiple
identical small chains. What I did was:

- I generated the peptides with pymol
- Generated a .gro with pdb2gmx

This step is "generating a molecular topology". You don't need a .gro -
it's just a regularized coordinate file produced as a side-effect.


Very much right. Thanks.


- Used editconf to create translated copies

Try genconf to do the replication. That should remove much of the manual
labour. You would still probably need to edit in the chain IDs yourself,
but that's easy work with a script or good editor.


Thanks!


- Stitching them together and creating the complete file, adjusting
numbers etc. manually

It worked well, but the chains are not recognized as *different* chains
-which could be useful. Documentation says I should use another format
like the pdb, but it is a bit sparse on the subject. I think I can use
pdb instead of gro if needed, but does this also work when creating
boxes etc.? Isn't there a way to get chain identifiers in a gro file?
What is best practice?

What do you want the chain identifiers for? I'm not aware of a
post-pdb2gmx purpose that they might serve.


This is where my naivety probably enters in: Analysis programs work on
groups. If several chains are defined, can each of these count as a
group? Indeed, chapter 8 doesn't explicitly say so, but... My intention
is to get analysis for each chain in my system. What is best practice
for that / where should I look in the docs?



They can, but you have to define them.  If there are multiple protein chains in 
the system, the Gromacs tools will define them as one group - 'Protein' - and 
not distinguish between them.  This is a rather easy problem to solve, though, 
without even using chain identifiers.  You can create index groups based on 
residue numbers to define each chain, then it doesn't matter what format the 
coordinate file is in.  For example, you can define groups like:


r 1-37
r 38-299

etc.

-Justin


If your system is N identical peptides in a solvent, then best practice
for generating a complete .top is to generate one for a single peptide
in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a
coordinate file which contains the N peptides' coordinates followed by
all the solvent (e.g. genconf - genbox). Then edit the [ molecules ]
section of the original .top to match. Other solutions are possible, but
require more involved use of pdb2gmx, and might indeed want chain IDs.


Uh, thanks. Not sure to have understood all of it, but I will do my
homework before coming back :)

m.
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] What is best way to get multiple chains?

2009-10-14 Thread ms
Mark Abraham ha scritto:
> ms wrote:
>> Hi,
>>
>> I am a gmx newbie, so please don't bite too much! :)
>>
>> Learning gmx, I am experimenting with simulations with multiple
>> identical small chains. What I did was:
>>
>> - I generated the peptides with pymol
>> - Generated a .gro with pdb2gmx
> 
> This step is "generating a molecular topology". You don't need a .gro -
> it's just a regularized coordinate file produced as a side-effect.

Very much right. Thanks.

>> - Used editconf to create translated copies
> 
> Try genconf to do the replication. That should remove much of the manual
> labour. You would still probably need to edit in the chain IDs yourself,
> but that's easy work with a script or good editor.

Thanks!

>> - Stitching them together and creating the complete file, adjusting
>> numbers etc. manually
>>
>> It worked well, but the chains are not recognized as *different* chains
>> -which could be useful. Documentation says I should use another format
>> like the pdb, but it is a bit sparse on the subject. I think I can use
>> pdb instead of gro if needed, but does this also work when creating
>> boxes etc.? Isn't there a way to get chain identifiers in a gro file?
>> What is best practice?
> 
> What do you want the chain identifiers for? I'm not aware of a
> post-pdb2gmx purpose that they might serve.

This is where my naivety probably enters in: Analysis programs work on
groups. If several chains are defined, can each of these count as a
group? Indeed, chapter 8 doesn't explicitly say so, but... My intention
is to get analysis for each chain in my system. What is best practice
for that / where should I look in the docs?

> If your system is N identical peptides in a solvent, then best practice
> for generating a complete .top is to generate one for a single peptide
> in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a
> coordinate file which contains the N peptides' coordinates followed by
> all the solvent (e.g. genconf - genbox). Then edit the [ molecules ]
> section of the original .top to match. Other solutions are possible, but
> require more involved use of pdb2gmx, and might indeed want chain IDs.

Uh, thanks. Not sure to have understood all of it, but I will do my
homework before coming back :)

m.
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Re: [gmx-users] What is best way to get multiple chains?

2009-10-13 Thread Mark Abraham

ms wrote:

Hi,

I am a gmx newbie, so please don't bite too much! :)

Learning gmx, I am experimenting with simulations with multiple
identical small chains. What I did was:

- I generated the peptides with pymol
- Generated a .gro with pdb2gmx


This step is "generating a molecular topology". You don't need a .gro - 
it's just a regularized coordinate file produced as a side-effect.



- Used editconf to create translated copies


Try genconf to do the replication. That should remove much of the manual 
labour. You would still probably need to edit in the chain IDs yourself, 
but that's easy work with a script or good editor.



- Stitching them together and creating the complete file, adjusting
numbers etc. manually

It worked well, but the chains are not recognized as *different* chains
-which could be useful. Documentation says I should use another format
like the pdb, but it is a bit sparse on the subject. I think I can use
pdb instead of gro if needed, but does this also work when creating
boxes etc.? Isn't there a way to get chain identifiers in a gro file?
What is best practice?


What do you want the chain identifiers for? I'm not aware of a 
post-pdb2gmx purpose that they might serve.


If your system is N identical peptides in a solvent, then best practice 
for generating a complete .top is to generate one for a single peptide 
in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a 
coordinate file which contains the N peptides' coordinates followed by 
all the solvent (e.g. genconf - genbox). Then edit the [ molecules ] 
section of the original .top to match. Other solutions are possible, but 
require more involved use of pdb2gmx, and might indeed want chain IDs.


Mark
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Re: [gmx-users] What is best way to get multiple chains?

2009-10-13 Thread Justin A. Lemkul



ms wrote:

Hi,

I am a gmx newbie, so please don't bite too much! :)

Learning gmx, I am experimenting with simulations with multiple
identical small chains. What I did was:

- I generated the peptides with pymol
- Generated a .gro with pdb2gmx
- Used editconf to create translated copies
- Stitching them together and creating the complete file, adjusting
numbers etc. manually

It worked well, but the chains are not recognized as *different* chains
-which could be useful. Documentation says I should use another format
like the pdb, but it is a bit sparse on the subject. I think I can use
pdb instead of gro if needed, but does this also work when creating
boxes etc.? Isn't there a way to get chain identifiers in a gro file?
What is best practice?


You can use .pdb format just fine.  There is no requirement that you use .gro, 
and in fact the format specification of .gro does not include a field for chain 
identifier, so no, there is no way to include chain identifiers in a .gro file.


-Justin



Thanks a lot,
Massimo
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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