Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Justin A. Lemkul]

C. Batistakis wrote:

Dear all

I am trying to visuallize a coarse-grained model  I have created (long 
bond length!) with VMD. I saw the script coarse_grain.tcl 
 but after 
many hours of trying I couldn't use it (I am a new user in VMD and I 
don't know how to source the script in VMD).




Open the Tk console and "source coarse_grain.tcl"


Can anybody give some more "for dummies" instructions?



There is also a simple Perl script here:

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD

-Justin


Thanks a lot!

Chrysostomos




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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[gmx-users] Coarse-Grain: GROMACS bond information to VMD

[C. Batistakis]

Dear all

I am trying to visuallize a coarse-grained model  I have created (long bond 
length!) with VMD. I saw the script coarse_grain.tcl but after many hours of 
trying I couldn't use it (I am a new user in VMD and I don't know how to source 
the script in VMD).

Can anybody give some more "for dummies" instructions?

Thanks a lot!

Chrysostomos


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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Mark Abraham]

Baofu Qiao wrote:

HI all,

I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD 
website. But both of them can only deal with single chain system. Take 
an example, if there are 10 proteins (+water) in my system,  how to 
convert to topology of the total system to .psf file? I tried to append 
the .psf. But VMD doesn't recognize the appended .psf file.


Find out how to generate a .psf using CHARMM/NAMD tools, then.

Mark
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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Nicolas Sapay]

Hello everybody,

Here is the rtf file I mentioned previously. It can be used by PSFGEN to 
generate a psf file from pdb files. The result can be used, for example, 
by the PME Electrostatics plugin of VMD. PSFGEN is available as a VMD 
plugin or as an independant executable.


Nicolas

Nicolas SAPAY a écrit :

Hi,

All TCL scripts dowloaded from the VMD website as well as mine are
supposed to be used within VMD. You have to run VMD first, then source the
script. Alternatively, you can source it in your .vmdrc file. After that,
you can run the g_cg function

Nicolas

  




  
  


HI all,

I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD
website. But both of them can only deal with single chain system. Take
an example, if there are 10 proteins (+water) in my system,  how to
convert to topology of the total system to .psf file? I tried to append
the .psf. But VMD doesn't recognize the appended .psf file.

Another question: 
How to use the code from Nicolas? I got the following error information
from 
 ./coarse_grain.tcl -tpr em.tpr

: command not found line 10:
./coarse_grain.tcl: line 14: proc: command not found
: command not found line 15:
./coarse_grain.tcl: line 17: global: command not found
./coarse_grain.tcl: line 18: global: command not found
./coarse_grain.tcl: line 19: global: command not found
./coarse_grain.tcl: line 20: global: command not found
./coarse_grain.tcl: line 21: global: command not found
./coarse_grain.tcl: line 22: global: command not found
./coarse_grain.tcl: line 23: global: command not found
./coarse_grain.tcl: line 24: global: command not found
./coarse_grain.tcl: line 25: global: command not found
: command not found line 26:
: command not found line 41:
: command not found line 45:
./coarse_grain.tcl: line 120: syntax error near unexpected token `}'
'/coarse_grain.tcl: line 120: ` } else {

best wishes,
Baofu Qiao

Nicolas SAPAY wrote:

  
Justin A. Lemkul wrote:


  I have also added a Perl script to the GROMACS site
(the VMD page):

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD";>http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD

The user provides an input topology file, and a .psf file is written,
which can be loaded as data for the structure in VMD.  The !NBOND
section seems to be the most important in this regard, so the other
sections are a bit rough, but it seems to work alright.

The caveat is the topology must be one generated by MARTINI, in order to
satisfy all the pattern matching and the order of the topology.  It
should be fairly easy to modify the program further to accommodate other
layouts, but I haven't had the need to do so.
  

I added text to the above page describing both scripts,
which are
attached. I'd have done that yesterday but the website was
intermittently down.

  
  
Thanks for posting the tcl script on the website, although this script has
been mainly coded by someone else. I have simply modified it for my own
purpose.

I also want to mention it is a good think to create a psf file if one work
with VMD. You store at once, bonds, atom types and charges. Actually, I
should have somewhere a .rtf file for the Martini amino acids and lipids
(the equivalent of the Gromacs rtp file for CHARMM). It can be used by
psfgen to generate a psf file with Martini bonds, charges and atom types.
If I can retrieve it in my archives, I will post it on the website.

Nicolas

  
  
Mark



  Nicolas Sapay wrote:
  
  
Hello Thomas,

I have a tcl script in my personal script library that might do what
you want to do. I didn't use it for quite a while, but it was working
well as far as I remember. I think it has been adapted from a script
available on the VMD website, but I don't remember exactly its
history. It doesn't seem too difficult to understand. You should be
able to modify it for your own purpose, if needed.

Cheers,
Nicolas


Thomas Schmidt a écrit :


  Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can
use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas


  

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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Nicolas SAPAY]

Hi,

All TCL scripts dowloaded from the VMD website as well as mine are
supposed to be used within VMD. You have to run VMD first, then source the
script. Alternatively, you can source it in your .vmdrc file. After that,
you can run the g_cg function

Nicolas

> 
> 
> 
>   
>   
> 
> 
> HI all,
> 
> I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD
> website. But both of them can only deal with single chain system. Take
> an example, if there are 10 proteins (+water) in my system,  how to
> convert to topology of the total system to .psf file? I tried to append
> the .psf. But VMD doesn't recognize the appended .psf file.
> 
> Another question: 
> How to use the code from Nicolas? I got the following error information
> from 
>  ./coarse_grain.tcl -tpr em.tpr
> 
> : command not found line 10:
> ./coarse_grain.tcl: line 14: proc: command not found
> : command not found line 15:
> ./coarse_grain.tcl: line 17: global: command not found
> ./coarse_grain.tcl: line 18: global: command not found
> ./coarse_grain.tcl: line 19: global: command not found
> ./coarse_grain.tcl: line 20: global: command not found
> ./coarse_grain.tcl: line 21: global: command not found
> ./coarse_grain.tcl: line 22: global: command not found
> ./coarse_grain.tcl: line 23: global: command not found
> ./coarse_grain.tcl: line 24: global: command not found
> ./coarse_grain.tcl: line 25: global: command not found
> : command not found line 26:
> : command not found line 41:
> : command not found line 45:
> ./coarse_grain.tcl: line 120: syntax error near unexpected token `}'
> '/coarse_grain.tcl: line 120: ` } else {
> 
> best wishes,
> Baofu Qiao
> 
> Nicolas SAPAY wrote:
>   cite="mid:49e9485f32667c27440f5b0b836a3bf4.squir...@webmail.cermav.cnrs.fr"
>  type="cite">
>   
> Justin A. Lemkul wrote:
> 
> 
>   I have also added a Perl script to the GROMACS site
> (the VMD page):
>
>  href="http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD";>http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD
>
> The user provides an input topology file, and a .psf file is written,
> which can be loaded as data for the structure in VMD.  The !NBOND
> section seems to be the most important in this regard, so the other
> sections are a bit rough, but it seems to work alright.
>
> The caveat is the topology must be one generated by MARTINI, in order to
> satisfy all the pattern matching and the order of the topology.  It
> should be fairly easy to modify the program further to accommodate other
> layouts, but I haven't had the need to do so.
>   
> 
> I added text to the above page describing both scripts,
> which are
> attached. I'd have done that yesterday but the website was
> intermittently down.
> 
>   
>   
> Thanks for posting the tcl script on the website, although this script has
> been mainly coded by someone else. I have simply modified it for my own
> purpose.
>
> I also want to mention it is a good think to create a psf file if one work
> with VMD. You store at once, bonds, atom types and charges. Actually, I
> should have somewhere a .rtf file for the Martini amino acids and lipids
> (the equivalent of the Gromacs rtp file for CHARMM). It can be used by
> psfgen to generate a psf file with Martini bonds, charges and atom types.
> If I can retrieve it in my archives, I will post it on the website.
>
> Nicolas
>
>   
>   
> Mark
>
> 
> 
>   Nicolas Sapay wrote:
>   
>   
> Hello Thomas,
>
> I have a tcl script in my personal script library that might do what
> you want to do. I didn't use it for quite a while, but it was working
> well as far as I remember. I think it has been adapted from a script
> available on the VMD website, but I don't remember exactly its
> history. It doesn't seem too difficult to understand. You should be
> able to modify it for your own purpose, if needed.
>
> Cheers,
> Nicolas
>
>
> Thomas Schmidt a écrit :
> 
> 
>   Dear Omer,
>
> many thanks for your answer, but your solution doesn't work for me.
> We have Protein-Lipid models in the CG scale.
> Only if I replace all atom names in the PDB file through "CA" I can
> use
> the "trace" drawing method, but get also wrong atoms connected to each
> other. For example CG Beads with low distances to each other, e.g. in
> coarse-grained benzene rings, were not connected. I guess that this
> method is distance dependent, too, but in another way. :-)
>
> Does anybody else have a solution (...to put GROMACS bond information
> into VMD)?
>
> Thomas
>
>
>   
> 
> ___
> gmx-users mailing list href="mailto:gmx-users@gromacs.org";>gmx-users@gromacs.org
>  href="http://lists.gromacs.org/mailman/listinfo/gmx-users";>http://lists.gromacs.org/mailman/listinfo/gmx-users
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> before
> posting!
> Please

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Justin A. Lemkul]

Baofu Qiao wrote:

HI all,

I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD 
website. But both of them can only deal with single chain system. Take 
an example, if there are 10 proteins (+water) in my system,  how to 
convert to topology of the total system to .psf file? I tried to append 
the .psf. But VMD doesn't recognize the appended .psf file.




I can't comment on Nicolas' script, but as for my own, you need to supply a 
single topology, there is no way to append the output.  You could, for 
visualization purposes, separate the coordinates of each of your subunits from 
the assembled structure, generate the corresponding .psf file for each, and load 
them all separately into VMD.  A little tedious, I know, but given the method 
for generating MARTINI topologies, I'm not sure I can provide a better method.


-Justin


Another question:
How to use the code from Nicolas? I got the following error information 
from

  ./coarse_grain.tcl -tpr em.tpr

: command not found line 10:
./coarse_grain.tcl: line 14: proc: command not found
: command not found line 15:
./coarse_grain.tcl: line 17: global: command not found
./coarse_grain.tcl: line 18: global: command not found
./coarse_grain.tcl: line 19: global: command not found
./coarse_grain.tcl: line 20: global: command not found
./coarse_grain.tcl: line 21: global: command not found
./coarse_grain.tcl: line 22: global: command not found
./coarse_grain.tcl: line 23: global: command not found
./coarse_grain.tcl: line 24: global: command not found
./coarse_grain.tcl: line 25: global: command not found
: command not found line 26:
: command not found line 41:
: command not found line 45:
./coarse_grain.tcl: line 120: syntax error near unexpected token `}'
'/coarse_grain.tcl: line 120: ` } else {

best wishes,
Baofu Qiao

Nicolas SAPAY wrote:

Justin A. Lemkul wrote:


I have also added a Perl script to the GROMACS site (the VMD page):

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD

The user provides an input topology file, and a .psf file is written,
which can be loaded as data for the structure in VMD.  The !NBOND
section seems to be the most important in this regard, so the other
sections are a bit rough, but it seems to work alright.

The caveat is the topology must be one generated by MARTINI, in order to
satisfy all the pattern matching and the order of the topology.  It
should be fairly easy to modify the program further to accommodate other
layouts, but I haven't had the need to do so.
  

I added text to the above page describing both scripts, which are
attached. I'd have done that yesterday but the website was
intermittently down.



Thanks for posting the tcl script on the website, although this script has
been mainly coded by someone else. I have simply modified it for my own
purpose.

I also want to mention it is a good think to create a psf file if one work
with VMD. You store at once, bonds, atom types and charges. Actually, I
should have somewhere a .rtf file for the Martini amino acids and lipids
(the equivalent of the Gromacs rtp file for CHARMM). It can be used by
psfgen to generate a psf file with Martini bonds, charges and atom types.
If I can retrieve it in my archives, I will post it on the website.

Nicolas

  

Mark



Nicolas Sapay wrote:
  

Hello Thomas,

I have a tcl script in my personal script library that might do what
you want to do. I didn't use it for quite a while, but it was working
well as far as I remember. I think it has been adapted from a script
available on the VMD website, but I don't remember exactly its
history. It doesn't seem too difficult to understand. You should be
able to modify it for your own purpose, if needed.

Cheers,
Nicolas


Thomas Schmidt a écrit :


Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can
use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas


  

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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Baofu Qiao]

HI all,

I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD
website. But both of them can only deal with single chain system. Take
an example, if there are 10 proteins (+water) in my system,  how to
convert to topology of the total system to .psf file? I tried to append
the .psf. But VMD doesn't recognize the appended .psf file.

Another question: 
How to use the code from Nicolas? I got the following error information
from 
 ./coarse_grain.tcl -tpr em.tpr

: command not found line 10:
./coarse_grain.tcl: line 14: proc: command not found
: command not found line 15:
./coarse_grain.tcl: line 17: global: command not found
./coarse_grain.tcl: line 18: global: command not found
./coarse_grain.tcl: line 19: global: command not found
./coarse_grain.tcl: line 20: global: command not found
./coarse_grain.tcl: line 21: global: command not found
./coarse_grain.tcl: line 22: global: command not found
./coarse_grain.tcl: line 23: global: command not found
./coarse_grain.tcl: line 24: global: command not found
./coarse_grain.tcl: line 25: global: command not found
: command not found line 26:
: command not found line 41:
: command not found line 45:
./coarse_grain.tcl: line 120: syntax error near unexpected token `}'
'/coarse_grain.tcl: line 120: ` } else {

best wishes,
Baofu Qiao

Nicolas SAPAY wrote:

  
Justin A. Lemkul wrote:


  I have also added a Perl script to the GROMACS site (the VMD page):

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD

The user provides an input topology file, and a .psf file is written,
which can be loaded as data for the structure in VMD.  The !NBOND
section seems to be the most important in this regard, so the other
sections are a bit rough, but it seems to work alright.

The caveat is the topology must be one generated by MARTINI, in order to
satisfy all the pattern matching and the order of the topology.  It
should be fairly easy to modify the program further to accommodate other
layouts, but I haven't had the need to do so.
  

I added text to the above page describing both scripts, which are
attached. I'd have done that yesterday but the website was
intermittently down.

  
  
Thanks for posting the tcl script on the website, although this script has
been mainly coded by someone else. I have simply modified it for my own
purpose.

I also want to mention it is a good think to create a psf file if one work
with VMD. You store at once, bonds, atom types and charges. Actually, I
should have somewhere a .rtf file for the Martini amino acids and lipids
(the equivalent of the Gromacs rtp file for CHARMM). It can be used by
psfgen to generate a psf file with Martini bonds, charges and atom types.
If I can retrieve it in my archives, I will post it on the website.

Nicolas

  
  
Mark



  Nicolas Sapay wrote:
  
  
Hello Thomas,

I have a tcl script in my personal script library that might do what
you want to do. I didn't use it for quite a while, but it was working
well as far as I remember. I think it has been adapted from a script
available on the VMD website, but I don't remember exactly its
history. It doesn't seem too difficult to understand. You should be
able to modify it for your own purpose, if needed.

Cheers,
Nicolas


Thomas Schmidt a écrit :


  Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can
use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas


  

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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Nicolas SAPAY]

> Justin A. Lemkul wrote:
>>
>> I have also added a Perl script to the GROMACS site (the VMD page):
>>
>> http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD
>>
>> The user provides an input topology file, and a .psf file is written,
>> which can be loaded as data for the structure in VMD.  The !NBOND
>> section seems to be the most important in this regard, so the other
>> sections are a bit rough, but it seems to work alright.
>>
>> The caveat is the topology must be one generated by MARTINI, in order to
>> satisfy all the pattern matching and the order of the topology.  It
>> should be fairly easy to modify the program further to accommodate other
>> layouts, but I haven't had the need to do so.
>
> I added text to the above page describing both scripts, which are
> attached. I'd have done that yesterday but the website was
> intermittently down.

Thanks for posting the tcl script on the website, although this script has
been mainly coded by someone else. I have simply modified it for my own
purpose.

I also want to mention it is a good think to create a psf file if one work
with VMD. You store at once, bonds, atom types and charges. Actually, I
should have somewhere a .rtf file for the Martini amino acids and lipids
(the equivalent of the Gromacs rtp file for CHARMM). It can be used by
psfgen to generate a psf file with Martini bonds, charges and atom types.
If I can retrieve it in my archives, I will post it on the website.

Nicolas

>
> Mark
>
>> Nicolas Sapay wrote:
>>> Hello Thomas,
>>>
>>> I have a tcl script in my personal script library that might do what
>>> you want to do. I didn't use it for quite a while, but it was working
>>> well as far as I remember. I think it has been adapted from a script
>>> available on the VMD website, but I don't remember exactly its
>>> history. It doesn't seem too difficult to understand. You should be
>>> able to modify it for your own purpose, if needed.
>>>
>>> Cheers,
>>> Nicolas
>>>
>>>
>>> Thomas Schmidt a écrit :
 Dear Omer,

 many thanks for your answer, but your solution doesn't work for me.
 We have Protein-Lipid models in the CG scale.
 Only if I replace all atom names in the PDB file through "CA" I can
 use
 the "trace" drawing method, but get also wrong atoms connected to each
 other. For example CG Beads with low distances to each other, e.g. in
 coarse-grained benzene rings, were not connected. I guess that this
 method is distance dependent, too, but in another way. :-)

 Does anybody else have a solution (...to put GROMACS bond information
 into VMD)?

 Thomas


>>>
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
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-- 
[ Nicolas Sapay - Post-Doctoral Fellow ]
CERMAV - www.cermav.cnrs.fr
BP53, 38041 Grenoble cedex 9, France
Phone: +33 (0)4 76 03 76 44/53

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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Mark Abraham]

Justin A. Lemkul wrote:


I have also added a Perl script to the GROMACS site (the VMD page):

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD

The user provides an input topology file, and a .psf file is written, 
which can be loaded as data for the structure in VMD.  The !NBOND 
section seems to be the most important in this regard, so the other 
sections are a bit rough, but it seems to work alright.


The caveat is the topology must be one generated by MARTINI, in order to 
satisfy all the pattern matching and the order of the topology.  It 
should be fairly easy to modify the program further to accommodate other 
layouts, but I haven't had the need to do so.


I added text to the above page describing both scripts, which are 
attached. I'd have done that yesterday but the website was 
intermittently down.


Mark


Nicolas Sapay wrote:

Hello Thomas,

I have a tcl script in my personal script library that might do what 
you want to do. I didn't use it for quite a while, but it was working 
well as far as I remember. I think it has been adapted from a script 
available on the VMD website, but I don't remember exactly its 
history. It doesn't seem too difficult to understand. You should be 
able to modify it for your own purpose, if needed.


Cheers,
Nicolas


Thomas Schmidt a écrit :

Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas

  


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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Justin A. Lemkul]

I have also added a Perl script to the GROMACS site (the VMD page):

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD

The user provides an input topology file, and a .psf file is written, which can 
be loaded as data for the structure in VMD.  The !NBOND section seems to be the 
most important in this regard, so the other sections are a bit rough, but it 
seems to work alright.


The caveat is the topology must be one generated by MARTINI, in order to satisfy 
all the pattern matching and the order of the topology.  It should be fairly 
easy to modify the program further to accommodate other layouts, but I haven't 
had the need to do so.


-Justin

Nicolas Sapay wrote:

Hello Thomas,

I have a tcl script in my personal script library that might do what you 
want to do. I didn't use it for quite a while, but it was working well 
as far as I remember. I think it has been adapted from a script 
available on the VMD website, but I don't remember exactly its history. 
It doesn't seem too difficult to understand. You should be able to 
modify it for your own purpose, if needed.


Cheers,
Nicolas


Thomas Schmidt a écrit :

Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas

  


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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: Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Thomas Schmidt]

Dear Nicholas,

great!!!
I've needed a bit time for testing but this works fine.
Many thanks for that script.

Thomas

-- 
Thomas H. Schmidt, PhD student
Computational Structural Biology
Chair of Life Science Informatics, B-IT
LIMES-Institute, University of Bonn
Dahlmannstrasse 2, D-53113 Bonn, Germany

Phone: +49-(0)228-2699 323
Fax: +49-(0)228-2699 341
http://www.csb.bit.uni-bonn.de


On Mo, 2009-10-19 at 16:53 +0200, Nicolas Sapay wrote:
> Hello Thomas,
> 
> I have a tcl script in my personal script library that might do what you 
> want to do. I didn't use it for quite a while, but it was working well 
> as far as I remember. I think it has been adapted from a script 
> available on the VMD website, but I don't remember exactly its history. 
> It doesn't seem too difficult to understand. You should be able to 
> modify it for your own purpose, if needed.
> 
> Cheers,
> Nicolas
> 
> 
> Thomas Schmidt a écrit :
> > Dear Omer,
> >
> > many thanks for your answer, but your solution doesn't work for me.
> > We have Protein-Lipid models in the CG scale.
> > Only if I replace all atom names in the PDB file through "CA" I can use
> > the "trace" drawing method, but get also wrong atoms connected to each
> > other. For example CG Beads with low distances to each other, e.g. in
> > coarse-grained benzene rings, were not connected. I guess that this
> > method is distance dependent, too, but in another way. :-)
> >
> > Does anybody else have a solution (...to put GROMACS bond information
> > into VMD)?
> >
> > Thomas

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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Nicolas Sapay]

Hello Thomas,

I have a tcl script in my personal script library that might do what you 
want to do. I didn't use it for quite a while, but it was working well 
as far as I remember. I think it has been adapted from a script 
available on the VMD website, but I don't remember exactly its history. 
It doesn't seem too difficult to understand. You should be able to 
modify it for your own purpose, if needed.


Cheers,
Nicolas


Thomas Schmidt a écrit :

Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas

  
##
#  TCL Script to visualize CG structures in VMD
#  
#  Version 3.0
##
#  
# Adapted from vmds
#
##

# 
==
# SETUP THE CG REPRESENTATION
# 
==
proc g_cg { args } {

### Some variable need to be global to the file
global helix_radius
global helix_color
global helix_angle
global helix_angle_tol
global CG_bb
global CG_bb_index
global CG_bb_num
global CG_prot_res
global bond

### Set defaults
set NAME"\[ g_cg \]"
set molid   top;# Molecule Id
set first   0;  # The first 
frame to process
set last-1; # The last 
frame to process
set skip1;  # The step 
between 2 frames
set nframe  0;  # number of 
frame
set sel_list{{name W WF} {name "BH.*" "SH.*"} {not name W 
WF "BH.*" "SH.*"}};   # Selection list
set rep_list{Lines Licorice Lines}; 
# Representation list
set color_list  {"ColorId 0" "ColorId 7" "ColorId 10"}; 
# Color list
set calpha  "name \"BH.*\"";# Calpha 
Selection text
set other   "not name \"BH.*\" \"SH.*\"";   # Non-Protein 
Selection text
set tpr "topol.tpr";# GROMACS TPR 
file
set helix_radius3;  # Cylinder 
representation for helix
set helix_color "red";
set helix_angle 57.0;   # Helix 
definition parameters
set helix_angle_tol 5.0;# Helix 
definition parameters
set gdistrib"/usr/export/gromacs-3.3.3";# GROMACS 
distribution

### Print Help message if no args
if {[llength $args] == 0} {
puts "Synopsis:"
puts "="
puts "  Rebuild the bonds between th particles of a coarse 
grained system"
puts "  Require a a GROMACS topology file and gmxdump"
puts ""
puts "Usage:"
puts "=="
puts "  g_cg \[options] -tpr a/gromacs/tpr/file.tpr"
puts ""
puts "Options:"
puts ""
puts "  -molid  top 
Molecule Id"
puts "  -tprtopo.tprGROMACS 
tolopolgy file corresping to your system"
puts "  -selsee below   List of 
the selections to display"
puts "  -repsee below   List of 
the representations to apply on each selection"
puts "  -color  see below   List of 
the color to apply on each selection"
puts "  -calpha name \"BH.*\"   Calpha 
particle (for the helical residues detection)"
puts "  -hangle 57.0Angle 
applied to retrieve helical residues"
puts "  -htol   5.0 Angle 
tolerance applied to retrieve helical residue"
puts "  -hradius3   Radius

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Mark Abraham]

Thomas Schmidt wrote:

Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?


No, but you can change the bond length heuristic VMD uses to guess where 
bonds are. See its manual or mailing list archives, I guess.


Mark
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Re: Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Thomas Schmidt]

Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas

-- 
Thomas H. Schmidt, PhD student
Computational Structural Biology
Chair of Life Science Informatics, B-IT
LIMES-Institute, University of Bonn
Dahlmannstrasse 2, D-53113 Bonn, Germany

Phone: +49-(0)228-2699 323
Fax: +49-(0)228-2699 341
http://www.csb.bit.uni-bonn.de



On Sa, 2009-10-17 at 18:16 +0200, Omer Markovitch wrote:
> What I do is visualize as trace. Than all the coarse-grained sphere
> are connected. Hope it helps. Omer.
>  
> Koby Levy research group,
> Weizmann Institute of Science. 
> FAX: 972-77-444-7905
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
> 
> 
> On Fri, Oct 16, 2009 at 11:24, Thomas Schmidt
>  wrote:
> Dear all,
> 
> is there any possibility to give the bond information out of
> GROMACS
> files to VMD? Especially for coarse-grained models (using the
> MARTINI
> FF) this would be a nice feature for visualization.
> 
> But in that case the distance analysis doesn't work, because
> we will
> always have too high distances between two particles (CG
> scale). If I
> use "Dynamic Bonds" (as described in this thread:
> 
> http://oldwww.gromacs.org/pipermail/gmx-users/2008-September/036124.html) VMD 
> draws bonds also between non-bonded particles.
> 
> I know that there is no official solutions for this
> (http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD),
> but maybe
> anybody of you has a script to convert *.top/*.itp/*.rtp files
> with a
> corresponding *.gro file into the PDB format with connectivity
> section
> or into the (NAMD) *.psf format. (?)
> The solution that I've found (top2psd.pl) is not smart enough
> because
> it's a simple 1-to-1 conversion of GROMACS topology files and
> has not
> the ability to replicate (and renumber) the topological data
> of single
> molecules (http://baaden.free.fr/soft/compchem.html).
> 
> Thanks for your help...
> Thomas
> 
> --
> Thomas H. Schmidt, PhD student
> Computational Structural Biology
> Chair of Life Science Informatics, B-IT
> LIMES-Institute, University of Bonn
> Dahlmannstrasse 2, D-53113 Bonn, Germany
> 
> Phone: +49-(0)228-2699 323
> Fax: +49-(0)228-2699 341
> http://www.csb.bit.uni-bonn.de
> 
> 
> ___
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> Please search the archive at http://www.gromacs.org/search
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> Can't post? Read
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> 

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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Omer Markovitch]

What I do is visualize as trace. Than all the coarse-grained sphere
are connected. Hope it helps. Omer.

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Fri, Oct 16, 2009 at 11:24, Thomas Schmidt wrote:

> Dear all,
>
> is there any possibility to give the bond information out of GROMACS
> files to VMD? Especially for coarse-grained models (using the MARTINI
> FF) this would be a nice feature for visualization.
>
> But in that case the distance analysis doesn't work, because we will
> always have too high distances between two particles (CG scale). If I
> use "Dynamic Bonds" (as described in this thread:
> http://oldwww.gromacs.org/pipermail/gmx-users/2008-September/036124.html)
> VMD draws bonds also between non-bonded particles.
>
> I know that there is no official solutions for this
> (http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD), but maybe
> anybody of you has a script to convert *.top/*.itp/*.rtp files with a
> corresponding *.gro file into the PDB format with connectivity section
> or into the (NAMD) *.psf format. (?)
> The solution that I've found (top2psd.pl) is not smart enough because
> it's a simple 1-to-1 conversion of GROMACS topology files and has not
> the ability to replicate (and renumber) the topological data of single
> molecules (http://baaden.free.fr/soft/compchem.html).
>
> Thanks for your help...
> Thomas
>
> --
> Thomas H. Schmidt, PhD student
> Computational Structural Biology
> Chair of Life Science Informatics, B-IT
> LIMES-Institute, University of Bonn
> Dahlmannstrasse 2, D-53113 Bonn, Germany
>
> Phone: +49-(0)228-2699 323
> Fax: +49-(0)228-2699 341
> http://www.csb.bit.uni-bonn.de
>
>
> ___
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[gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Thomas Schmidt]

Dear all,

is there any possibility to give the bond information out of GROMACS
files to VMD? Especially for coarse-grained models (using the MARTINI
FF) this would be a nice feature for visualization.

But in that case the distance analysis doesn't work, because we will
always have too high distances between two particles (CG scale). If I
use "Dynamic Bonds" (as described in this thread:
http://oldwww.gromacs.org/pipermail/gmx-users/2008-September/036124.html) VMD 
draws bonds also between non-bonded particles.

I know that there is no official solutions for this
(http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD), but maybe
anybody of you has a script to convert *.top/*.itp/*.rtp files with a
corresponding *.gro file into the PDB format with connectivity section
or into the (NAMD) *.psf format. (?)
The solution that I've found (top2psd.pl) is not smart enough because
it's a simple 1-to-1 conversion of GROMACS topology files and has not
the ability to replicate (and renumber) the topological data of single
molecules (http://baaden.free.fr/soft/compchem.html).

Thanks for your help...
Thomas

-- 
Thomas H. Schmidt, PhD student
Computational Structural Biology
Chair of Life Science Informatics, B-IT
LIMES-Institute, University of Bonn
Dahlmannstrasse 2, D-53113 Bonn, Germany

Phone: +49-(0)228-2699 323
Fax: +49-(0)228-2699 341
http://www.csb.bit.uni-bonn.de


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