[gmx-users] (no subject)

[Yang Ye]

Use -s A.gro or -s B.tpr. They could be your original structure file.

Eva Priego wrote:

>Dear David,
>
>I have tried a lot of options. I can get the .xtc file but for the .pdb file I
>need the .tpr file.
>
>What is the problem?.
>
>
>
>Thanks
>
>
>
>
>
>
>
>  
>
>>On Mon, 2005-09-19 at 16:43 +0000, Eva Priego wrote:
>>    
>>
>
>  
>
>>>Dear users,
>>>      
>>>
>
>  
>
>
>  
>
>>>I have concatenated two trajectory files from a crashed md and I would like
>>>      
>>>
>to
>
>  
>
>>>convert it to a .pdb file. When I use the trjconv command I get this error:
>>>      
>>>
>
>  
>
>
>  
>
>
>  
>
>
>  
>
>>>trjconv_d -f hlab.trr -o hlabmd.pdb
>>>      
>>>
>
>  
>
>
>  
>
>>>Will write pdb: Protein data bank file
>>>      
>>>
>
>  
>
>
>  
>
>>>Fatal error: File topol.tpr not found
>>>      
>>>
>
>  
>
>
>
>
>
>
>
>
>  
>
>
>  
>
>
>  
>
>>>As I have rerun the md I have two .tpr files, the initial one before the
>>>      
>>>
>crash
>
>  
>
>>>and the one  I have created with tpbconv to continue the md.
>>>      
>>>
>
>  
>
>
>  
>
>>>Which one do I have to put in trjconv?. I am using gromacs 3.2.1
>>>      
>>>
>
>  
>
>
>  
>
>>run trjconv_d -h to see options
>>    
>>
>
>  
>
>>(or any other program)
>>    
>>
>
>  
>
>
>  
>
>
>  
>
>>>Thanks in advance
>>>      
>>>
>
>  
>
>
>  
>
>
>  
>
>
>  
>
>>>Eva
>>>      
>>>
>
>  
>
>>>---------------------------------------
>>>      
>>>
>
>  
>
>
>  
>
>>>Dr. Eva Maria Priego
>>>      
>>>
>
>  
>
>
>  
>
>>>Department of Biochemistry. University of Cambridge
>>>      
>>>
>
>  
>
>
>  
>
>>>80 Tennis Court Road. Cambridge CB2 1GA. U.K.
>>>      
>>>
>
>  
>
>
>  
>
>>>e-mail:evamaria at cryst.bioc.cam.ac.uk
>>>      
>>>
>
>  
>
>
>  
>
>>>_______________________________________________
>>>      
>>>
>
>  
>
>>>gmx-users mailing list
>>>      
>>>
>
>  
>
>>>gmx-users at 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 gmx-users-request at gromacs.org.
>>>      
>>>
>
>  
>
>>-- 
>>    
>>
>
>  
>
>>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
>>    
>>
>
>  
>
>>spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>>    
>>
>
>  
>
>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>    
>>
>
>  
>
>
>  
>
>>_______________________________________________
>>    
>>
>
>  
>
>>gmx-users mailing list
>>    
>>
>
>  
>
>>gmx-users at 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 gmx-users-request at gromacs.org.
>>    
>>
>
>  
>
>
>---------------------------------------
>
>Dr. Eva Maria Priego
>
>Department of Biochemistry. University of Cambridge
>
>80 Tennis Court Road. Cambridge CB2 1GA. U.K.
>
>e-mail:evamaria at cryst.bioc.cam.ac.uk
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at 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 gmx-users-request at gromacs.org.
>
>  
>