Re: [gmx-users] hi

[Shima Arasteh]

Hi,
Welcome! :-) Sincerely,
Shima



 From: marzieh dehghan 
To: gmx-users@gromacs.org 
Sent: Thursday, September 20, 2012 10:11 PM
Subject: [gmx-users] hi
 

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Re: [gmx-users] hi

[lina]

On May 29, 2011, at 20:45, rashi.pari...@gmail.com wrote:

> Hi all..
> I want to ask if it is possible to restart the md run if due to power problem 
> final md run not completed means initiating md from where is stop due to any 
> reason?

Suppose your .tpr is topol.tpr

mdrun -cpi state.cpt 

Or suppose your .tpr is my.tpr

You may try

mdrun -deffnm my -cpi my.cpt 

As suggested by others. Start learning read mdrun --h

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Re: [gmx-users] hi

[Mark Abraham]

On 29/05/2011 10:45 PM, rashi.pari...@gmail.com wrote:

Hi all..
I want to ask if it is possible to restart the md run if due to power 
problem final md run not completed means initiating md from where is 
stop due to any reason? 


Please use a meaningful subject line in emails. See 
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts


Mark
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Re: Re: [gmx-users] hi

[rashi . parihar]

thanx sarath 4r reply..can u expalin little bit more..I did not get from  
mdrun -h.


On , Sarath Chandra Dantu  wrote:



On 29 May 2011 14:45, rashi.pari...@gmail.com> wrote:




Hi all..
I want to ask if it is possible to restart the md run if due to power  
problem final md run not completed means initiating md from where is stop  
due to any reason?



You can supply the checkpoint file written out, by -cpi option to mdrun  
and continue your simulation. For more information




mdrun -h.




Best Wishes,




Sarath




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Re: [gmx-users] hi

[Sarath Chandra Dantu]

On 29 May 2011 14:45,  wrote:

> Hi all..
> I want to ask if it is possible to restart the md run if due to power
> problem final md run not completed means initiating md from where is stop
> due to any reason?
>

You can supply the checkpoint file written out, by -cpi option to mdrun and
continue your simulation. For more information see
mdrun -h.

Best Wishes,

Sarath

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Re: [gmx-users] Hi

[David van der Spoel]

On 2010-08-07 15.22, poj...@icp.uni-stuttgart.de wrote:

Hi,

I am starting with GROMACS. About the units in GROMACS,
I read in the manual that one can use the reduced units
for lennard-jones systems. It means that if I want to use
reduce units I just write the values of all the parameters
(distance, mass, charge ...) in reduced units for all
files (.mdp, .gro , .top) and all will be right? After
making the appropiate conversion for the temperature:

1 reduced unit of temperature = 120.271

Or should I need to specify in some place that I am using
reduced units?

Thanks.


That is correct.

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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Re: [gmx-users] HI

[Justin A. Lemkul]

Please use a descriptive subject line.  Simply using "Hi" will often not attract 
the attention of someone who can help you, and other times will get trapped in a 
spam filter, depending on the settings of the server or email client.


pavan payghan wrote:
I have to recreate .gro file from .trr file by using trjconv which i 
have deleated previously for disk  space reasons ,  im using following  
commond for that


trjconv -f full.trr -s full.tpr -o fullout.gro .

   so my question is will this commond give me the same gro file that it 
was previously or it may variate

or any changes that u suggest in the given commond.



No, this will give you the entire trajectory in .gro format, which is likely a 
very large file.  Use gmxcheck to see for yourself.



my second question is regarding g_rms,
i created the .xvg for  g_rms , the grph shows  it has  continous 
run for molecule with some peaks in  between why is it so as im doing 
analysis for the first time i dont know what does this indicates .
 is it because  the molecule is jumping across the box ? so that more 
rmsd at that place

  ,i think by using -nojump i can do this  ?



That depends on what you define as a peak.  Small spikes may or may not be 
reasonable, depending on what your structure is doing.  If these spikes are very 
large, they could correspond to your molecule crossing PBC, in which case you 
would have to use trjconv.


-Justin

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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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Re: [gmx-users] Hi

[XAvier Periole]

try the option -ignh, it will ignore the the hydrogen atoms in your
pdb file and generate the ones necessary to the force field you choose.

On Dec 15, 2009, at 9:52 AM, ashish pandey wrote:


Dear all,
my self ashish and i am trying to dynamics using gromacs.
i am new in these field. in the time of running Pdb2gmx to create .gro
file. i am geting these error.

Fatal error:
Atom HA in residue MET 1 not found in rtp entry with 9 atoms

please help me sortout these problem.

--  
Ashish Pandey

NIPER India
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Re: [gmx-users] Hi

[Justin A. Lemkul]

Please choose an informative subject line pertinent to the content of your 
message; messages that have simply greetings often get blocked by spam filters, 
and furthermore do not often rouse the interest of someone who may be able to 
help you.


pawan raghav wrote:
Which files should be downloaded to use GRACE and in which directory 
should be installed to use xmgrace command.




Please go to the Grace homepage, as I have told you before.  There, you will 
find links to how to download Grace, instructions on how to install it 
(including a complete Users Guide!), and information about help forums.  That is 
the better place to post your questions, since this list is for communication 
directly related to Gromacs.


Also realize, that on any forum, a question as simple as "how do I do the 
following..." is unlikely to get much specific help, unless you can demonstrate 
that you've made some effort to help yourself (as in, you have a specific 
problem, which you can articulate in terms of the commands used, output 
received, etc).


I would strongly suggest having a thorough read of the following:

http://www.catb.org/%7Eesr/faqs/smart-questions.html

-Justin

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Re: [gmx-users] hi

[Justin A. Lemkul]

Please choose an informative subject line, as it will help attract the attention 
of someone interested in helping you.


PAVAN RELISH DESTINY RESOLVING CRUX OF LIFE. wrote:

 I am new to Gromacs & using it with Amber force field amber03,
 i am able 2 run my system of DNA till steepest descent but 
when i tried to run it for cg it showed 
 that can not work with so much of  constrains so i tried to 
run it with -Dposres  


Minimization with position restraints serves very little, if any, purpose in my 
mind.


 directly to mdrun with md integrator it showed an error 
message "wrote pdb files with previous & current 
 co-ordinate segmentation fault." 
 how can i 
modify my mdp file to overcome this problem ?


Your system is insufficiently minimized and/or equilibrated.  Please see the 
following:


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

-Justin

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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] hi questions about installing GROMACS

[Justin A. Lemkul]

Amit Choubey wrote:

hi,

I am trying to install GROMACS (version 4.0) on my local machine. I 
tried to follow the supplied simple instruction in the INSTALL file. The 
./configure step works but the "make" command doesnt work. My bash 
prints out  "make: *** No targets specified and no makefile found.  Stop."  



Then probably configuration didn't actually work, if you have no Makefile.  A 
few things to consider:


1. Use the latest version of Gromacs (4.0.5), not a version that is nearly a 
year old.  You will get the latest features and bug fixes.
2. Ensure that you have read/write access in the directory you're trying to run 
the commands.


-Justin

What should i do for this? Should i save the GROMACS Directory somewhere 
else?



Amit




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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] hi

[Mark Abraham]

Moutusi Manna wrote:

 I want to perform simulation of transmembrane
peptide. I have a perseuillibrated POPO (hydrated)
bilayer (using CHARMM),containing more than 32,000
atom. But when I try to convert ".pdb" to ".gro" using
"pdb2gmx", it shows the following error


The role of pdb2gmx is not convert a .pdb to a .gro, it is to generate a 
topology file from a structure file. It outputs a structure file that is 
consistent with that topology file, but that structure file can be in 
several formats. See pdb2gmx -h.



Fatal error:
Residue "popc" not found in residue topology detabase

Please suggest how I can overcome this problem .


http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

If this makes no sense (and even if it does) reading relevant parts of 
chapter 5 of the GROMACS manual will be needed here.


Mark
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Re: [gmx-users] Hi All..one question about charge making

[Mark Abraham]

uki zhu wrote:

Dear all gmx-users,
Sorry to bother you.
I am trying to make a molecule with a unit charge well-distributed. But 
I do not know how to write such *.top file. Does every atom get the same 
charge at the beginning? And can we use Gromacs to simulate the changes 
of the charge distribution?


I don't understand what you're trying to do, or why you think GROMACS is 
suited for doing it.


Mark
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Re: [gmx-users] hi

[SeungPyo Hong]

On 8/15/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
>
> vinod kumar wrote:
> > Hi, gmx-users,
> >
> > HI , how to overcome this problem
> > the output after grompp if em.mdp 
> >> fatal error : number of coordinates in coordinate file ( solvated.gro8655)
> >> does not match topology ( top.top 8657)
> >
> > i have made necessary changes in the .top file with respect to the out
> > put of genbox .
>
> It seems that you have either used a different .top file, or not changed
> it correctly. Go back a step and try again.
>
> Mark
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I sometimes have that problem when adding ligand with using Dundee server.
Checking the number of atoms in the .pdb(or .gro) file and its .itp file
might be helpful.
When using Dundee server they give you the .gro file with all the hydrogen
bound.
But they give you 3 .pdb file.

-- 
--
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many object.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
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Re: [gmx-users] hi

[Mark Abraham]

vinod kumar wrote:

Hi, gmx-users,

HI , how to overcome this problem
the output after grompp if em.mdp 

fatal error : number of coordinates in coordinate file ( solvated.gro 8655)
does not match topology ( top.top 8657)


i have made necessary changes in the .top file with respect to the out
put of genbox .


It seems that you have either used a different .top file, or not changed 
it correctly. Go back a step and try again.


Mark
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Re: [gmx-users] Hi all

[Mark Abraham]

ann rose wrote:

Hi

I am new to Gromacs.
I would like to simulate oligoether branched polysiloxanes in gromacs. I 
have the force field availble for the same
Whether gromacs will support force filed for polymers containing hetreo 
atmos like silicon?


Yes - this information is part of the force field.


If so how can I incoroprate this into gromacs?


You will need a thorough working knowledge of at least chapter 5 of the 
manual, and plenty from earlier sections. This will also let you assess 
whether the range of functions computed by gromacs is suitable for your 
forcefield.



and also
How to get the starting configuration for the poysiloxanes? ( like .gro, 
.top, .itp files)


.gro files are structure files... you're responsible for generating 
them. Search the mailing list for suggestions.


.top files can be generated by pdb2gmx if you can generate suitable .rtp 
monomers, but life may be messy here for branched polymers... you may 
need to make these by hand.


.itp files are included by .top files and include your basic force field 
files as well as regularly recycled units like solvents... you need to 
make these.


Mark
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Re: [gmx-users] Hi...

[Navratna Vajpai]

As suggested by you I tried using the g_angle. But got tucked. It asks for a .ndx file. I tried making it using mk_angndx but gave me an error when i used the option -type phi-psi. Although it worked well when I used the option dihedral instead of phi-psi. The .ndx file has strange nomenclature which i didn't followed. [ Phi=180.0_2_33.5 ] or [ Phi=0.0_3_3.77 ] Please suggest.As you said problem with the analysis program g_rama. I looked for g_rama as well as g_chi .. its mentioned in the g_chi option that the phi psi calculation are different from the conventional calculations. Instead of C'(i-1)-Ni-CAi-C'i , H-N-CA-C' is used and similarly its different for the psi as well. But it also states that it is different from the g_rama. I was wondering what other atoms are taken for the phi-psi calculations?Best regards NavOn Sep 14, 2006, at 4:22 PM, David van der Spoel wrote:Navratna Vajpai wrote: Sorry for not so explicitly explaining the things.. Here it goesI have a nona peptide and I ran a MD of 20ns using OPLS-AA force field. when I used the OPLS-AA the phi angles came out to be -ve for three of the amino acids. which is stericaly not allowed. But when I ran it using GROMOS I found all the phi-psi combinations with a negative phi value distribution. But now I am lost as you have said it works only for GROMOS like force field. Why? problem in the anaysis program (assuming you used g_rama). please use g_angle. and if that so I have got -ve phi distribution for the other phi-psi plots. My other question remained unanswered even now. Is there any way really to judge which force field is to be chosen for particular type of analysis?Best regards Thanks what do you mean with -ve ?force field can be evaluated in many ways.Start by checking this paper and references in them:Hydration thermodynamic properties of amino Acid analogues: a systematic comparison of biomolecular force fields and water models.    * Hess B,    * van der Vegt NF.J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2006 Sep 7;110(35):17616-26.-- David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596,  	75124 Uppsala, Swedenphone:	46 18 471 4205		fax: 46 18 511 755[EMAIL PROTECTED]	[EMAIL PROTECTED]   http://folding.bmc.uu.se___gmx-users mailing list    gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php  ***Navratna VajpaiPh. D student in Prof. Grzesiek's laboratoryDepartment of Structural BiologyBiozentrum, University of BaselKlingelbergstrasse 70,CH-4056Basel, Switzerland.Phone- +41 61 267 2080(O)	       +41 78 744 0810(M)[EMAIL PROTECTED] ___
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Re: [gmx-users] Hi...

[Navratna Vajpai]

You are right .. I have used g_rama for the phi-psi values. I will try g_angle as well. With -ve i meant negative values for the phi angle. As far as I understand negative phi values are sterically  not allowed. let me check with the g_angle as well. Thanks for the answer as well the reference. best regardsNavOn Sep 14, 2006, at 4:22 PM, David van der Spoel wrote:Navratna Vajpai wrote: Sorry for not so explicitly explaining the things.. Here it goesI have a nona peptide and I ran a MD of 20ns using OPLS-AA force field. when I used the OPLS-AA the phi angles came out to be -ve for three of the amino acids. which is stericaly not allowed. But when I ran it using GROMOS I found all the phi-psi combinations with a negative phi value distribution. But now I am lost as you have said it works only for GROMOS like force field. Why? problem in the anaysis program (assuming you used g_rama). please use g_angle. and if that so I have got -ve phi distribution for the other phi-psi plots. My other question remained unanswered even now. Is there any way really to judge which force field is to be chosen for particular type of analysis?Best regards Thanks what do you mean with -ve ?force field can be evaluated in many ways.Start by checking this paper and references in them:Hydration thermodynamic properties of amino Acid analogues: a systematic comparison of biomolecular force fields and water models.    * Hess B,    * van der Vegt NF.J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2006 Sep 7;110(35):17616-26.-- David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596,  	75124 Uppsala, Swedenphone:	46 18 471 4205		fax: 46 18 511 755[EMAIL PROTECTED]	[EMAIL PROTECTED]   http://folding.bmc.uu.se___gmx-users mailing list    gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php  ***Navratna VajpaiPh. D student in Prof. Grzesiek's laboratoryDepartment of Structural BiologyBiozentrum, University of BaselKlingelbergstrasse 70,CH-4056Basel, Switzerland.Phone- +41 61 267 2080(O)	       +41 78 744 0810(M)[EMAIL PROTECTED] ___
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Re: [gmx-users] Hi...

[David van der Spoel]

Navratna Vajpai wrote:

Sorry for not so explicitly explaining the things.. Here it goes
I have a nona peptide and I ran a MD of 20ns using OPLS-AA force field. 
when I used the OPLS-AA the phi angles came out to be -ve for three of 
the amino acids. which is stericaly not allowed. But when I ran it using 
GROMOS I found all the phi-psi combinations with a negative phi value 
distribution. But now I am lost as you have said it works only for 
GROMOS like force field. Why?


problem in the anaysis program (assuming you used g_rama). please use 
g_angle.


and if that so I have got -ve phi distribution for the other phi-psi plots. 
My other question remained unanswered even now. Is there any way really 
to judge which force field is to be chosen for particular type of analysis?
Best regards 
Thanks




what do you mean with -ve ?

force field can be evaluated in many ways.

Start by checking this paper and references in them:

Hydration thermodynamic properties of amino Acid analogues: a systematic 
comparison of biomolecular force fields and water models.


* Hess B,
* van der Vegt NF.

J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2006 Sep 
7;110(35):17616-26.


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] Hi...

[David van der Spoel]

Mu Yuguang (Dr) wrote:
OPLS-aa force field is good for beta structure, it is not so good for 
alpha helix study.


Amber99f force field is good for alpha helix , but not good for beta 
structure



Very encouraging...



--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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RE: [gmx-users] Hi...

[Mu Yuguang (Dr)]

OPLS-aa force field is good for beta
structure, it is not so good for alpha helix study.

Amber99f force field is good for alpha
helix , but not good for beta structure

 



Best regards

Yuguang

 

Dr. Yuguang Mu

Assistant Professor

School of Biological Sciences

Nanyang Technological University

60 Nanyang Drive  Singapore
637551 Tel: +65-63162885 Fax: +65-67913856

http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php

 











From:
[EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Navratna Vajpai
Sent: Thursday, September 14, 2006
9:50 PM
To: Discussion
 list for GROMACS users
Subject: Re: [gmx-users] Hi...



 

Sorry for not so explicitly explaining the things.. Here it
goes



I have a nona peptide and I ran a MD of 20ns using OPLS-AA force
field. 





when I used the OPLS-AA the phi angles came out to be -ve for three of
the amino acids. which is stericaly not allowed. But when I ran it using
GROMOS I found all the phi-psi combinations with a negative phi value
distribution. But now I am lost as you have said it works only for GROMOS like
force field. Why?





and if that so I have got -ve phi distribution for the other phi-psi
plots. 





My other question remained unanswered even now. Is there any way
really to judge which force field is to be chosen for particular type of
analysis?





Best regards 





Thanks





 





On Sep 14, 2006, at 3:36 PM, David van der Spoel wrote:









Navratna Vajpai wrote:







Hi all.. I wrote this mail yesterday. But could not receive any reply
till now. So if someone can suggest something about it. That would be nice.
Best regards





Nav





Begin forwarded message:







*From: *Navratna Vajpai <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>





*Date: *September 13, 2006 10:32:21 AM GMT+02:00





*To: *Discussion list for GROMACS users
mailto:gmx-users@gromacs.org>>





*Subject: **[gmx-users] Hi...*





*Reply-To: *Discussion list for GROMACS users
mailto:gmx-users@gromacs.org>>





 





Dear All





Hi.. This is in regard to your previously replied mail regarding the
use of GROMOS96 or OPLS-AA or AMBER force field.





As you said it depends upon the users taste which one to use. This
means that the three on a broad manner should give convergence of the analyzed
data set. Infact from my simulation runs using oplss-aa and gromos96, I didn't
found that. I tried using the GROMOS96 and opls-aa force field on my small
peptides for a period of 20ns and found that with opls-aa even the phi-psi
combination of the individual amino acids were incorrect. Actually this always
puzzled me to make a choice for the Force field.  The rest of the script was unchanged
for the two runs.





Could you please comment on the above results? Is there any way really
to judge which force field is to be chosen for particular type of analysis?





Best regards





Nav





 









 





 





what do you mean with incorrect? your question is quite vague.





 





the g_rama program works only for GROMOS like force fields
unfortunately but that doesn't mean the phi/psi are wrong. What would be the
"correct" result anyway? Maybe your peptide unfolds.





 





-- 





David.











David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,





Dept. of Cell and Molecular Biology, Uppsala University.





Husargatan 3, Box
 596,    75124 Uppsala, Sweden





phone:  46 18 471 4205   fax: 46 18 511 755





[EMAIL PROTECTED]  [EMAIL PROTECTED]   http://folding.bmc.uu.se











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***





Navratna
Vajpai





Ph.
D student in Prof. Grzesiek's laboratory





Department
of Structural Biology





Biozentrum, University of Basel





Klingelbergstrasse
70,





CH-4056





Basel, Switzerland.





Phone-
+41 61 267 2080(O)





      
    +41 78 744 0810(M)





 





[EMAIL PROTECTED]





 











 








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Re: [gmx-users] Hi...

[Navratna Vajpai]

Sorry for not so explicitly explaining the things.. Here it goesI have a nona peptide and I ran a MD of 20ns using OPLS-AA force field. when I used the OPLS-AA the phi angles came out to be -ve for three of the amino acids. which is stericaly not allowed. But when I ran it using GROMOS I found all the phi-psi combinations with a negative phi value distribution. But now I am lost as you have said it works only for GROMOS like force field. Why?and if that so I have got -ve phi distribution for the other phi-psi plots. My other question remained unanswered even now. Is there any way really to judge which force field is to be chosen for particular type of analysis?Best regards ThanksOn Sep 14, 2006, at 3:36 PM, David van der Spoel wrote:Navratna Vajpai wrote: Hi all.. I wrote this mail yesterday. But could not receive any reply till now. So if someone can suggest something about it. That would be nice. Best regardsNavBegin forwarded message: *From: *Navratna Vajpai <[EMAIL PROTECTED] >*Date: *September 13, 2006 10:32:21 AM GMT+02:00*To: *Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>*Subject: **[gmx-users] Hi...**Reply-To: *Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>Dear AllHi.. This is in regard to your previously replied mail regarding the use of GROMOS96 or OPLS-AA or AMBER force field.As you said it depends upon the users taste which one to use. This means that the three on a broad manner should give convergence of the analyzed data set. Infact from my simulation runs using oplss-aa and gromos96, I didn't found that. I tried using the GROMOS96 and opls-aa force field on my small peptides for a period of 20ns and found that with opls-aa even the phi-psi combination of the individual amino acids were incorrect. Actually this always puzzled me to make a choice for the Force field.  The rest of the script was unchanged for the two runs.Could you please comment on the above results? Is there any way really to judge which force field is to be chosen for particular type of analysis?Best regardsNav what do you mean with incorrect? your question is quite vague.the g_rama program works only for GROMOS like force fields unfortunately but that doesn't mean the phi/psi are wrong. What would be the "correct" result anyway? Maybe your peptide unfolds.-- David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596,  	75124 Uppsala, Swedenphone:	46 18 471 4205		fax: 46 18 511 755[EMAIL PROTECTED]	[EMAIL PROTECTED]   http://folding.bmc.uu.se___gmx-users mailing list    gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php  ***Navratna VajpaiPh. D student in Prof. Grzesiek's laboratoryDepartment of Structural BiologyBiozentrum, University of BaselKlingelbergstrasse 70,CH-4056Basel, Switzerland.Phone- +41 61 267 2080(O)	       +41 78 744 0810(M)[EMAIL PROTECTED] ___
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Re: [gmx-users] Hi ..

[David van der Spoel]

Navratna Vajpai wrote:

Dear Prof. David
Thanks for the suggestion. I just had a look for the various force field 
options. before starting my simulation I have a little queries..
1) Can I not use the same GROMOS force field g43b1 and then add HA 
afterwards by any other software or any other program in your package?

No, that would be meaningless.

2)Can I use ffoplsaa (all atom force field) for the vacuum simulation? 
or should I use ffencadv for the simulation?


ffoplsaa is fine as long as you look into the protonation state of the 
side chains which is non-trivial.


3) What does scaled-down vacuum charges mean? Is it different from the 
normal vacuum force field?


neutralized side chains usually.


Many thanks and regards


Please read the following papers:

@Article{Jorgensen96a,
  author =   {W. L. Jorgensen and D. S. Maxwell and J. {Tirado-Rives}},
  title = 	 {Development and testing of the {OPLS} all-atom force field 
on conformational energetics and properties of organic liquids},

  journal =  {J. Am. Chem. Soc.},
  year = 1996,
  volume =   118,
  pages ={11225-11236}
}

@Article{Jorgensen2005a,
  author =   {William L. Jorgensen and Julian Tirado-Rives},
  title = 	 {Potential energy functions for atomic-level simulations of 
water and organic and biomolecular systems},

  journal =  {Proc. Natl. Acad. Sci. USA},
  year = 2005,
  volume =   102,
  pages ={6665-6670 }
}

@Article{Christen2005a,
  author = 	 {Markus Christen and Philippe H. H{\"u}nenberger and Dirk 
Bakowies and Riccardo Baron and Roland B{\"u}rgi and Daan P. Geerke and 
Tim N. Heinz and Mika A. Kastenholz and Vincent Kr{\"a}utler and Chris 
Oostenbrink and Christine Peter and Daniel Trzesniak and Wilfred F. van 
Gunsteren},

  title ={The GROMOS software for biomolecular simulation: GROMOS05},
  journal =  {J. Comp. Chem.},
  year = 2005,
  volume =   26,
  pages ={1719-1751}
}





Nav
 On Aug 17, 2006, at 9:11 AM, David van der Spoel wrote:


Navratna Vajpai wrote:

Dear Mark
Hello.
The force field I used is g43b1 from GROMOS96. I checked the 
g43b1.atp file and fond that the HC is defined there which 
corresponds to Hydrogen attached to the Carbon. But somehow in the 
pdb outcome this is not there. the output pdb file contains only H 
atoms corresponding to HN. Now I exactly don't know which type of 
atoms are defined there. Kindly let me know what should I do to bring 
HA into the scene. 

use an all atom force field.


Best regards
Nav
On Aug 17, 2006, at 5:46 AM, Mark Abraham wrote:

Navratna Vajpai wrote:
Dear All I have been able to carry on with the MD run of my 
peptides. But when I converted the traj into the pdb file I 
realized that there are no HA atoms in the pdb. I checked the rtp 
file and found that even those atoms are not defined there. So can 
anyone tell me how to get the HA (after or before the MD run) as i 
need them explicitly . I was trying to look for the options 
available in the trjconv but could not find.

Thanks and regards


Does your force field include explicit non-polar hydrogen atoms? Or 
does it use united atoms?


Mark
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***
Navratna Vajpai
Ph. D student in Prof. Grzesiek's laboratory
Department of Structural Biology
Biozentrum, University of Basel
Klingelbergstrasse 70,
CH-4056
Basel, Switzerland.
Phone- +41 61 267 2080(O)
   +41 78 744 0810(M)
[EMAIL PROTECTED] 

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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED]  [EMAIL PROTECTED]   
http://folding.bmc.uu.se


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Re: [gmx-users] Hi ..

[Navratna Vajpai]

Dear Prof. DavidThanks for the suggestion. I just had a look for the various force field options. before starting my simulation I have a little queries..1) Can I not use the same GROMOS force field g43b1 and then add HA afterwards by any other software or any other program in your package?2)Can I use ffoplsaa (all atom force field) for the vacuum simulation? or should I use ffencadv for the simulation?3) What does scaled-down vacuum charges mean? Is it different from the normal vacuum force field?Many thanks and regardsNav On Aug 17, 2006, at 9:11 AM, David van der Spoel wrote:Navratna Vajpai wrote: Dear MarkHello.The force field I used is g43b1 from GROMOS96. I checked the g43b1.atp file and fond that the HC is defined there which corresponds to Hydrogen attached to the Carbon. But somehow in the pdb outcome this is not there. the output pdb file contains only H atoms corresponding to HN. Now I exactly don't know which type of atoms are defined there. Kindly let me know what should I do to bring HA into the scene.  use an all atom force field. Best regardsNavOn Aug 17, 2006, at 5:46 AM, Mark Abraham wrote: Navratna Vajpai wrote: Dear All I have been able to carry on with the MD run of my peptides. But when I converted the traj into the pdb file I realized that there are no HA atoms in the pdb. I checked the rtp file and found that even those atoms are not defined there. So can anyone tell me how to get the HA (after or before the MD run) as i need them explicitly . I was trying to look for the options available in the trjconv but could not find.Thanks and regards Does your force field include explicit non-polar hydrogen atoms? Or does it use united atoms?Mark___gmx-users mailing list    gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php ***Navratna VajpaiPh. D student in Prof. Grzesiek's laboratoryDepartment of Structural BiologyBiozentrum, University of BaselKlingelbergstrasse 70,CH-4056Basel, Switzerland.Phone- +41 61 267 2080(O)       +41 78 744 0810(M)[EMAIL PROTECTED] ___gmx-users mailing list    gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596,  	75124 Uppsala, Swedenphone:	46 18 471 4205		fax: 46 18 511 755[EMAIL PROTECTED]	[EMAIL PROTECTED]   http://folding.bmc.uu.se___gmx-users mailing list    gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php  ***Navratna VajpaiPh. D student in Prof. Grzesiek's laboratoryDepartment of Structural BiologyBiozentrum, University of BaselKlingelbergstrasse 70,CH-4056Basel, Switzerland.Phone- +41 61 267 2080(O)	       +41 78 744 0810(M)[EMAIL PROTECTED] ___
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Re: [gmx-users] Hi ..

[David van der Spoel]

Navratna Vajpai wrote:

Dear Mark
Hello.
The force field I used is g43b1 from GROMOS96. I checked the g43b1.atp 
file and fond that the HC is defined there which corresponds to Hydrogen 
attached to the Carbon. But somehow in the pdb outcome this is not 
there. the output pdb file contains only H atoms corresponding to HN. 
Now I exactly don't know which type of atoms are defined there. Kindly 
let me know what should I do to bring HA into the scene. 

use an all atom force field.


Best regards
Nav

On Aug 17, 2006, at 5:46 AM, Mark Abraham wrote:


Navratna Vajpai wrote:
Dear All I have been able to carry on with the MD run of my peptides. 
But when I converted the traj into the pdb file I realized that there 
are no HA atoms in the pdb. I checked the rtp file and found that 
even those atoms are not defined there. So can anyone tell me how to 
get the HA (after or before the MD run) as i need them explicitly . I 
was trying to look for the options available in the trjconv but could 
not find.

Thanks and regards


Does your force field include explicit non-polar hydrogen atoms? Or 
does it use united atoms?


Mark
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***
Navratna Vajpai
Ph. D student in Prof. Grzesiek's laboratory
Department of Structural Biology
Biozentrum, University of Basel
Klingelbergstrasse 70,
CH-4056
Basel, Switzerland.
Phone- +41 61 267 2080(O)
   +41 78 744 0810(M)

[EMAIL PROTECTED] 






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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] Hi ..

[Navratna Vajpai]

Dear MarkHello.The force field I used is g43b1 from GROMOS96. I checked the g43b1.atp file and fond that the HC is defined there which corresponds to Hydrogen attached to the Carbon. But somehow in the pdb outcome this is not there. the output pdb file contains only H atoms corresponding to HN. Now I exactly don't know which type of atoms are defined there. Kindly let me know what should I do to bring HA into the scene. Best regardsNavOn Aug 17, 2006, at 5:46 AM, Mark Abraham wrote:Navratna Vajpai wrote: Dear All I have been able to carry on with the MD run of my peptides. But when I converted the traj into the pdb file I realized that there are no HA atoms in the pdb. I checked the rtp file and found that even those atoms are not defined there. So can anyone tell me how to get the HA (after or before the MD run) as i need them explicitly . I was trying to look for the options available in the trjconv but could not find.Thanks and regards Does your force field include explicit non-polar hydrogen atoms? Or does it use united atoms?Mark___gmx-users mailing list    gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php  ***Navratna VajpaiPh. D student in Prof. Grzesiek's laboratoryDepartment of Structural BiologyBiozentrum, University of BaselKlingelbergstrasse 70,CH-4056Basel, Switzerland.Phone- +41 61 267 2080(O)	       +41 78 744 0810(M)[EMAIL PROTECTED] ___
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Re: [gmx-users] Hi ..

[Mark Abraham]

Navratna Vajpai wrote:
Dear All 
I have been able to carry on with the MD run of my peptides. But when I 
converted the traj into the pdb file I realized that there are no HA 
atoms in the pdb. I checked the rtp file and found that even those atoms 
are not defined there. So can anyone tell me how to get the HA (after or 
before the MD run) as i need them explicitly . I was trying to look for 
the options available in the trjconv but could not find.

Thanks and regards


Does your force field include explicit non-polar hydrogen atoms? Or does 
it use united atoms?


Mark
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Re: [gmx-users] Hi..

[Navratna Vajpai]

Many thanks Eric, it worked. I didn't really had look into this.Best regardsNavOn Aug 16, 2006, at 11:34 AM, Erik Marklund wrote:On Wed, 2006-08-16 at 10:07 +0200, David van der Spoel wrote: Navratna Vajpai wrote: Hey Mark..I had attached the file along with the mail. I think you could not receive it. let me paste the contents and explain it little more. I am trying to run the simulation in vacuum of a nona peptide. I managed to get pdb2gmx working and even further the EM working. But when I tried to do the MD run after a small minimization of protein, I got an error message after the execution of grompp. The execution asked for the -n option which indicates for the index file. 1) I don't know why it asked for? My guess it's because of this line in the mdp file:tc-grps     =  protein      solApparently you have temperature-coupled the solvent, even though youhave no solvent. Vacuum, right? Note that grompp is looking for 'sol'and, when it can't find it among the default groups (see manual), itlooks for an index file:Fatal error:Group sol not found in indexfile.Maybe you have non-default goups in your mdp file, while not using the'-n' option of grompp.In that case use the '-n' option.Try removing 'sol' from the mdp file. If you are simulating in vacuum,you (probably) have no solvent./Erik 2) If it ask for is there any way to solv this problem. Actually i tried using that also. But the error stayed back. I am also pasting the error after the grompp. Somehow this could not prepare the input file for the MD run. 3) third question is: I am wondering whether i can start my run just after the execution of pdb2gmx. Any ways 1) the system is in vacuum and second while running it for quite long, minimization of energy will automatically take place. You should probably start by doing the tutorial and browsing the web site, check out the flow chart for doing simulations. -- Erik Marklund, PhD Student, Molecular Biopcysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596,          75124 Uppsala, Swedenphone: +46 18 471 4537          fax: +46 18 511 755[EMAIL PROTECTED]___gmx-users mailing list    gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php  ***Navratna VajpaiPh. D student in Prof. Grzesiek's laboratoryDepartment of Structural BiologyBiozentrum, University of BaselKlingelbergstrasse 70,CH-4056Basel, Switzerland.Phone- +41 61 267 2080(O)	       +41 78 744 0810(M)[EMAIL PROTECTED] ___
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Re: [gmx-users] Hi..

[Erik Marklund]

On Wed, 2006-08-16 at 10:07 +0200, David van der Spoel wrote:
> Navratna Vajpai wrote:
> > Hey Mark..
> > I had attached the file along with the mail. I think you could 
> > not receive it. let me paste the contents and explain it little more. 
> > I am trying to run the simulation in vacuum of a nona peptide. I managed 
> > to get pdb2gmx working and even further the EM working. But when I tried 
> > to do the MD run after a small minimization of protein, I got an error 
> > message after the execution of grompp. The execution asked for the -n 
> > option which indicates for the index file. 1) I don't know why it asked for?

My guess it's because of this line in the mdp file:
tc-grps =  protein  sol

Apparently you have temperature-coupled the solvent, even though you
have no solvent. Vacuum, right? Note that grompp is looking for 'sol'
and, when it can't find it among the default groups (see manual), it
looks for an index file:

Fatal error:
Group sol not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the
'-n' option of grompp.
In that case use the '-n' option.

Try removing 'sol' from the mdp file. If you are simulating in vacuum,
you (probably) have no solvent.

/Erik

> > 2) If it ask for is there any way to solv this problem. Actually i tried 
> > using that also. But the error stayed back. 
> > I am also pasting the error after the grompp. Somehow this could not 
> > prepare the input file for the MD run. 
> > 3) third question is: I am wondering whether i can start my run just 
> > after the execution of pdb2gmx. Any ways 1) the system is in vacuum and 
> > second while running it for quite long, minimization of energy will 
> > automatically take place.
> You should probably start by doing the tutorial and browsing the web 
> site, check out the flow chart for doing simulations.
-- 
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone: +46 18 471 4537  fax: +46 18 511 755
[EMAIL PROTECTED]

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Re: [gmx-users] Hi..

[David van der Spoel]

Navratna Vajpai wrote:

Hey Mark..
I had attached the file along with the mail. I think you could 
not receive it. let me paste the contents and explain it little more. 
I am trying to run the simulation in vacuum of a nona peptide. I managed 
to get pdb2gmx working and even further the EM working. But when I tried 
to do the MD run after a small minimization of protein, I got an error 
message after the execution of grompp. The execution asked for the -n 
option which indicates for the index file. 1) I don't know why it asked for?
2) If it ask for is there any way to solv this problem. Actually i tried 
using that also. But the error stayed back. 
I am also pasting the error after the grompp. Somehow this could not 
prepare the input file for the MD run. 
3) third question is: I am wondering whether i can start my run just 
after the execution of pdb2gmx. Any ways 1) the system is in vacuum and 
second while running it for quite long, minimization of energy will 
automatically take place.
You should probably start by doing the tutorial and browsing the web 
site, check out the flow chart for doing simulations.

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] Hi..

[Navratna Vajpai]

Hey Mark..I had attached the file along with the mail. I think you could not receive it. let me paste the contents and explain it little more. I am trying to run the simulation in vacuum of a nona peptide. I managed to get pdb2gmx working and even further the EM working. But when I tried to do the MD run after a small minimization of protein, I got an error message after the execution of grompp. The execution asked for the -n option which indicates for the index file. 1) I don't know why it asked for?2) If it ask for is there any way to solv this problem. Actually i tried using that also. But the error stayed back. I am also pasting the error after the grompp. Somehow this could not prepare the input file for the MD run. 3) third question is: I am wondering whether i can start my run just after the execution of pdb2gmx. Any ways 1) the system is in vacuum and second while running it for quite long, minimization of energy will automatically take place.**ERROR:Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#checking input for internal consistency...Generated 279 of the 1225 non-bonded parameter combinationsExcluding 3 bonded neighbours for Protein             1processing coordinates...double-checking input for internal consistency...Velocities were taken from a Maxwell distribution at 300 Krenumbering atomtypes...converting bonded parameters...Walking down the molecule graph to make shake-blocksinitialising group options...processing index file...---Program grompp, VERSION 3.3Source code file: readir.c, line: 775Fatal error:Group sol not found in indexfile.Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.In that case use the '-n' option.*#!/bin/csh# this is the demo moleculesetenv MOL ilepep### INTRODUCTION ###clear cat << _EOF_--Welcome to the GROMACS demo.This is a script that takes about 10 min to run.In this demo we will demonstrate how to simulate MolecularDynamics (MD) using the GROMACS software package.The demo will perform a complete molecular dynamics (MD) simulationof a small peptide in water. The only input file we need to do thisis a pdb file of a small peptide.If you have any problems or remarks with respect to this demonstration,please mail to: [EMAIL PROTECTED] , or check the resources onour website http://www.gromacs.org .--_EOF_echo -n "Press "set  ans = $< CHECK ENVIRONMENT clear cat << _EOF_--Before we you can actually start the GROMACS demo, the programsmust be present in your PATH. This might already be the case ifthey are linked to /usr/local/bin. If not, follow the instructionsin the getting started section. If GROMACS is not installed properly on your computer, contact your system manager.--_EOF_echo -n "Press "set  ans = $<## PDB2GMX ##clearcat << _EOF_--Before we can start any simulation we need a molecular toplogyfile. This topology file ( .top extension ) is generated by theprogram pdb2gmx. The only input file of the pdb2gmx program is the pdbfile of our peptide ( .pdb extension ). Because most pdb files do not contain all hydrogen atoms, the pdb2gmxprogram will also add them to our peptide. The output file whichcontains the structure of the peptide when hydrogen atoms are added is agromos structure file ( .gro extension )  --_EOF_if ( $?DISPLAY ) then	echo "You seem to have the DISPLAY variable is set, so we will"        echo "pop up a window with the output of the pdb2gmx program"  endifecho -n "Press "set  ans = $& ! output.pdb2gmxecho "pdb2gmx finished"echo -n "Press "set  ans = $<# GROMPP #clearcat << _EOF_--

Re: [gmx-users] Hi..

[Mark Abraham]

Navratna Vajpai wrote:
Dear All .. 
I have only recently started the GROMACS package. I want to run a MD 
simulation in vacuum for 5 ns say. I have tried to edit the demo file 
which comes with the GROMACS package. but Some how it give an error. 
Which I am still unable to solve. I am atttaching the file under this. 
Could any one please help me to move further. 
I am able to generate the .gro file and am able to run the pdb2gmx. 


OK at the moment you've done the analogue of calling the over-worked 
free car mechanic and said "My car is broken, tell me what's wrong". 
They are going to be much more likely to give you useful help if you 
tell them what you were trying to do, how you were trying to do it, and 
what the error was when you tried. Otherwise, they'll go and do 
something more interesting and/or profitable. :-)


Mark
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Re: [gmx-users] hi

[Nguyen Hoang Phuong]

> hi today i have tried to run the position restrained dynamics using my tpr 
> file
>  grompp -f pr.mdp -c 7/trp_b4pr.gro -p 1/trp.top -o 8/trp_pr.tpr
>
> But its showing the error
> Fatal error:
> number of coordinates in coordinate file (7/trp_b4pr.gro, 14580)
>  does not match topology (1/trp.top, 0)
>
>
> can anyone help me
sure! Please have a look at the files trp_b4pr.gro and trp.top. Then you
check if the number of atoms in the *gro file (written on the second
line) are the same with those in the *top file (written on the last
lines). Your can delete some atoms in the *gro files to match those of in
the *top file.

Phuong

>
> thanking you
> santosh
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Re: [gmx-users] Hi

[TJ Piggot]

Hi

I had the same problem i needed NA in the .gro (get this by in genion 
having -pname NA)


hope this help

Tom

--On Wednesday, April 05, 2006 15:38:22 +0200 Tsjerk Wassenaar 
<[EMAIL PROTECTED]> wrote:



Hi :)

Not the box, you probably need NA or NA+. It's case sensitive and depends
on the force field definition you use.

Cheers,

Tsjerk


On 4/5/06, Adriana Pietropaolo <[EMAIL PROTECTED]> wrote:

Probably you generated a bad box.
Check the box with i.e. rasmol  and try to use -princ option in editconf
(to put the protein in its inertial axes) and genion to make the ions to
ensure charge neutrality.
good luck,
Adriana


hi
today i have tried with some other protein but the problem still
persists . today i will tell you problem in detail

today i have taken the protein pdb file which conatains only the amino
acids no hetero atoms

i have run the pdb2gmx command
pdb2gmx -f 1.pdb -o 1/out1.top -p 1/out1.top -i 1/out1.itp -n
1/out1.ndx -q 1/out1.pdb

i got all the 5 files

later i used the command edit conf
 editconf -bt octahedron -f 1/out1.gro -o 2/out2.gro -c -d 0 .7

then i run the genbox
 genbox -cp 2/out2.gro -cs spc216.gro -o 3/out3.gro -p 1/out 1.top
here i got the gro file and modified top file

then i have run the grompp
 grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o 4/out4.tpr
 my mdp file is
bellow

##
title   =  drg_trp
cpp =  /usr/bin/cpp
define  =  -DFLEX_SPC
constraints =  none
integrator  =  steep
dt  =  0.002;  ps !
nsteps  =  1000
ns_type =  grid
rlist   =  0.9
coulombtype =  PME ; Use particle-mesh ewald
rcoulomb=  0.9
rvdw=  1.0
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  4
ewald_rtol  =  le-5
optimize_fft=  yes
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
;
;  Energy minimizing stuff
;
emtol   = 1000.0
emstep  =  0.01
###
There i got one NOTE : System has non-zero total charge: - 6.98e+00

later i tried to run the mdrun but the process fails at 24 steps

Then i used the genion

genion -s 4/out4.tpr -o 5/out5.gro -pname Na -np 7 -g 5/out 5.log

here i got the modified gro file
but tere was warning that
 turning of free energy, will use lambda=0
Then i have edited the top file i got according to the gro file
since i m using the gromacs 3.3 the #include ions.itp was default
so i have removed the 7 water atoms from the top file and added 7 Na
atoms and run the grompp

grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr
here the programme was failed showing the error
Fatal error:
No such moleculetype Na
i have checked the ions .itp
its having the information Na atom than why its showing this i could
n't understand
can any one help me over this here i have attatched my out6.gro file
and the top file

Thanking you
Santosh Naik
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--
_
Adriana Pietropaolo,
PhD student,
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
WEB:www2.fci.unibo.it/~adriana
Tel 051/6446992
FAX 051/2093690
_



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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336




--
TJ Piggot
[EMAIL PROTECTED]
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Re: [gmx-users] Hi

[bharat v. adkar]

Dear Santosh,
check what forcefield u have used...
whatever forcefield u use, add ions as per its recommended format 
specified in ions.itp. Read ions.itp carefully... if it is GROMOS96, 
u have to change Na to NA+ and likewise...


all the best...

bharat


On Wed, 5 Apr 2006, santosh naik wrote:


hi
today i have tried with some other protein but the problem still persists .
today i will tell you problem in detail

today i have taken the protein pdb file which conatains only the amino
acids no hetero atoms

i have run the pdb2gmx command
pdb2gmx -f 1.pdb -o 1/out1.top -p 1/out1.top -i 1/out1.itp -n
1/out1.ndx -q 1/out1.pdb

i got all the 5 files

later i used the command edit conf
editconf -bt octahedron -f 1/out1.gro -o 2/out2.gro -c -d 0 .7

then i run the genbox
genbox -cp 2/out2.gro -cs spc216.gro -o 3/out3.gro -p 1/out 1.top
here i got the gro file and modified top file

then i have run the grompp
grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o 4/out4.tpr
my mdp file is
bellow

##
title   =  drg_trp
cpp =  /usr/bin/cpp
define  =  -DFLEX_SPC
constraints =  none
integrator  =  steep
dt  =  0.002;  ps !
nsteps  =  1000
ns_type =  grid
rlist   =  0.9
coulombtype =  PME ; Use particle-mesh ewald
rcoulomb=  0.9
rvdw=  1.0
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  4
ewald_rtol  =  le-5
optimize_fft=  yes
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
;
;  Energy minimizing stuff
;
emtol   = 1000.0
emstep  =  0.01
###
There i got one NOTE : System has non-zero total charge: -6.98e+00

later i tried to run the mdrun but the process fails at 24 steps

Then i used the genion

genion -s 4/out4.tpr -o 5/out5.gro -pname Na -np 7 -g 5/out 5.log

here i got the modified gro file
but tere was warning that
turning of free energy, will use lambda=0
Then i have edited the top file i got according to the gro file
since i m using the gromacs 3.3 the #include ions.itp was default
so i have removed the 7 water atoms from the top file and added 7 Na atoms
and run the grompp

grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr
here the programme was failed showing the error
Fatal error:
No such moleculetype Na
i have checked the ions .itp
its having the information Na atom than why its showing this i could
n't understand
can any one help me over this here i have attatched my out6.gro file
and the top file

Thanking you
Santosh Naik
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Re: [gmx-users] Hi

[Mark Abraham]

santosh naik wrote:

grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr
here the programme was failed showing the error
Fatal error:
No such moleculetype Na
i have checked the ions .itp
its having the information Na atom than why its showing this i could
n't understand
can any one help me over this here i have attatched my out6.gro file
and the top file


gromacs is telling you the force field you are using doesn't have a 
molecule type of Na. This is distinct from an atom type of Na. Some 
force fields use SOD for the molecule type for sodium ions. Go and check 
the ions.itp file and adjust accordingly.


Adriana's reply might suggest why your minimization failed. Personally I 
wouldn't bother with PME for minimization, but I don't know whether 
switching to cut-off will help you.


Mark
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Re: [gmx-users] Hi

[Tsjerk Wassenaar]

Hi :)Not the box, you probably need NA or NA+. It's case sensitive and depends on the force field definition you use. Cheers,TsjerkOn 4/5/06, 
Adriana Pietropaolo <[EMAIL PROTECTED]> wrote:
Probably you generated a bad box.Check the box with i.e. rasmol  and try to use -princ option in editconf(to put the protein in its inertial axes) and genion to make the ions toensure charge neutrality.good luck,
Adriana> hi> today i have tried with some other protein but the problem still persists .> today i will tell you problem in detail>> today i have taken the protein pdb file which conatains only the amino
> acids no hetero atoms>> i have run the pdb2gmx command> pdb2gmx -f 1.pdb -o 1/out1.top -p 1/out1.top -i 1/out1.itp -n> 1/out1.ndx -q 1/out1.pdb>> i got all the 5 files
>> later i used the command edit conf>  editconf -bt octahedron -f 1/out1.gro -o 2/out2.gro -c -d 0 .7>> then i run the genbox>  genbox -cp 2/out2.gro -cs spc216.gro -o 3/out3.gro -p 1/out 
1.top> here i got the gro file and modified top file>> then i have run the grompp>  grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o 4/out4.tpr>  my mdp file is> bellow>
> ##> title   =  drg_trp> cpp =  /usr/bin/cpp> define  =  -DFLEX_SPC> constraints =  none
> integrator  =  steep> dt  =  0.002;  ps !> nsteps  =  1000> ns_type =  grid> rlist   =  0.9> coulombtype =  PME ; Use particle-mesh ewald
> rcoulomb=  0.9> rvdw=  1.0> fourierspacing  =  0.12> fourier_nx  =  0> fourier_ny  =  0> fourier_nz  =  0> pme_order   =  4
> ewald_rtol  =  le-5> optimize_fft=  yes> Tcoupl  =  no> Pcoupl  =  no> gen_vel =  no> ;> ;  Energy minimizing stuff
> ;> emtol   = 1000.0> emstep  =  0.01> ###> There i got one NOTE : System has non-zero total charge: -
6.98e+00>> later i tried to run the mdrun but the process fails at 24 steps>> Then i used the genion>> genion -s 4/out4.tpr -o 5/out5.gro -pname Na -np 7 -g 5/out 5.log>
> here i got the modified gro file> but tere was warning that>  turning of free energy, will use lambda=0> Then i have edited the top file i got according to the gro file> since i m using the gromacs 
3.3 the #include ions.itp was default> so i have removed the 7 water atoms from the top file and added 7 Na atoms> and run the grompp>> grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr
> here the programme was failed showing the error> Fatal error:> No such moleculetype Na> i have checked the ions .itp> its having the information Na atom than why its showing this i could
> n't understand> can any one help me over this here i have attatched my out6.gro file> and the top file>> Thanking you> Santosh Naik> ___
> gmx-users mailing listgmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the> www interface or send it to [EMAIL PROTECTED].> Can't post? Read 
http://www.gromacs.org/mailing_lists/users.php>--_Adriana Pietropaolo,PhD student,dipartimento di Chimica Fisica ed Inorganica,Facolta' di Chimica Industriale
Universita' di BolognaWEB:www2.fci.unibo.it/~adrianaTel 051/6446992FAX 051/2093690
gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of Groningen
Nijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336
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Re: [gmx-users] Hi

[Adriana Pietropaolo]

Probably you generated a bad box.
Check the box with i.e. rasmol  and try to use -princ option in editconf 
(to put the protein in its inertial axes) and genion to make the ions to 
ensure charge neutrality.
good luck,
Adriana

> hi
> today i have tried with some other protein but the problem still persists .
> today i will tell you problem in detail
> 
> today i have taken the protein pdb file which conatains only the amino
> acids no hetero atoms
> 
> i have run the pdb2gmx command
> pdb2gmx -f 1.pdb -o 1/out1.top -p 1/out1.top -i 1/out1.itp -n
> 1/out1.ndx -q 1/out1.pdb
> 
> i got all the 5 files
> 
> later i used the command edit conf
>  editconf -bt octahedron -f 1/out1.gro -o 2/out2.gro -c -d 0 .7
> 
> then i run the genbox
>  genbox -cp 2/out2.gro -cs spc216.gro -o 3/out3.gro -p 1/out 1.top
> here i got the gro file and modified top file
> 
> then i have run the grompp
>  grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o 4/out4.tpr
>  my mdp file is
> bellow
> 
> ##
> title   =  drg_trp
> cpp =  /usr/bin/cpp
> define  =  -DFLEX_SPC
> constraints =  none
> integrator  =  steep
> dt  =  0.002;  ps !
> nsteps  =  1000
> ns_type =  grid
> rlist   =  0.9
> coulombtype =  PME ; Use particle-mesh ewald
> rcoulomb=  0.9
> rvdw=  1.0
> fourierspacing  =  0.12
> fourier_nx  =  0
> fourier_ny  =  0
> fourier_nz  =  0
> pme_order   =  4
> ewald_rtol  =  le-5
> optimize_fft=  yes
> Tcoupl  =  no
> Pcoupl  =  no
> gen_vel =  no
> ;
> ;  Energy minimizing stuff
> ;
> emtol   = 1000.0
> emstep  =  0.01
> ###
> There i got one NOTE : System has non-zero total charge: -6.98e+00
> 
> later i tried to run the mdrun but the process fails at 24 steps
> 
> Then i used the genion
> 
> genion -s 4/out4.tpr -o 5/out5.gro -pname Na -np 7 -g 5/out 5.log
> 
> here i got the modified gro file
> but tere was warning that
>  turning of free energy, will use lambda=0
> Then i have edited the top file i got according to the gro file
> since i m using the gromacs 3.3 the #include ions.itp was default
> so i have removed the 7 water atoms from the top file and added 7 Na atoms
> and run the grompp
> 
> grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr
> here the programme was failed showing the error
> Fatal error:
> No such moleculetype Na
> i have checked the ions .itp
> its having the information Na atom than why its showing this i could
> n't understand
> can any one help me over this here i have attatched my out6.gro file
> and the top file
> 
> Thanking you
> Santosh Naik
> ___
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> www interface or send it to [EMAIL PROTECTED]
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> 

-- 
_
Adriana Pietropaolo,
PhD student,
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
WEB:www2.fci.unibo.it/~adriana
Tel 051/6446992
FAX 051/2093690 
_



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Re: [gmx-users] hi

[Tsjerk Wassenaar]

Hi Santosh,

For one thing, you don't want to use the gmx force field. For the rest,
you can safely listen to Lars ;) But it is in general good to read a
bit on the background of the force fields and to read papers regarding
the types of systems you are trying to simulate. From these you can aso
get a good idea about the other parameters to use. 

Cheers,

TsjerkOn 3/25/06, Lars Schaefer <[EMAIL PROTECTED]> wrote:
hi santosh,which force field to use usually dependes on your system. E.g., for DNA,the AMBER force field is often used. For proteins, you might want to useGROMOS96 or OPLS, which are quite popular these days. However, this does
not necessarily mean that the other force fields, such as GROMACS(ffgmx) are worse for your particular system.In principle, some force fields are all-atom (e.g., OPLS-AA) and somehave united atoms for aliphatic CHn groups, 
e.g. ffgmx.Larssantosh naik wrote:> hi friends>> i m santosh naik.friends i m new to this field so i m facing a lot of> problems dealing with this program.so i wants to start up with
> simple simulations like proteins in water. my problem is which force> field i should use in *pdb2gmx* is it default one or some other please> can any one will help me to solve my problem?>
> thanking you> santosh naik>>>>___>gmx-users mailing list
gmx-users@gromacs.org>http://www.gromacs.org/mailman/listinfo/gmx-users>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to [EMAIL PROTECTED].>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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.Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336
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Re: [gmx-users] hi

[Lars Schaefer]

hi santosh,
which force field to use usually dependes on your system. E.g., for DNA, 
the AMBER force field is often used. For proteins, you might want to use 
GROMOS96 or OPLS, which are quite popular these days. However, this does 
not necessarily mean that the other force fields, such as GROMACS 
(ffgmx) are worse for your particular system.
In principle, some force fields are all-atom (e.g., OPLS-AA) and some 
have united atoms for aliphatic CHn groups, e.g. ffgmx.
Lars 



santosh naik wrote:


hi friends
 
i m santosh naik.friends i m new to this field so i m facing a lot of 
problems dealing with this program.so i wants to start up with 
simple simulations like proteins in water. my problem is which force 
field i should use in *pdb2gmx* is it default one or some other please 
can any one will help me to solve my problem?
 
thanking you

santosh naik



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Re: [gmx-users] Hi all!

[David van der Spoel]

Marcelo Fabricio Masman wrote:

Hi all!!!
I am using the programme grompp (double precision) and the programme 
genion to make  "neutral" .top and .tpr files. But after change the 
quantity of H2O molecules and add the line with the necessary Na+ ions I 
am still having WARNING and the charge is STILL  negative. What happend? 
What am I doing wrong? Should I do something else?

Here are the WARNING banners:
 


Generated 243951 of the 243951 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
Excluding 2 bonded neighbours for SOL 41338
WARNING 1 [file "Ab-1.top", line 5860]:
  Too few parameters on line (source file toppush.c, line 1096)
Excluding 2 bonded neighbours for 3 Na+
WARNING 2 [file "Ab-1.top", line 5860]:
  System has non-zero total charge: -3.00e+00

processing coordinates...
WARNING 3 [file "Ab-1.top", line 5860]:
  Bad box in file Ab-1_n.gro


you have the wrong order of things in your topology file and you haven't 
updated the  number of atoms in the gro file (should be 6 fewer)



Generated a cubic box   10.898 x   10.838 x   10.922
double-checking input for internal consistency...
renumbering atomtypes...

Thank you very much.

Marcelo




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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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