[gmx-users] pdb2gmx -inter automatised ?

[Christian Fufezan]

Ok,

"pdb2gmx ....  < inter.txt" did the trick. Although it was a bit  
painful to generate the inter.txt in the first instance :)

Thanks again

Christian Fufezan


Dr. Christian Fufezan
Westfälische Wilhelms-Universität Münster
Institut für Biochemie und Biotechnologie der Pflanzen (IBBP)
Hindenburgplatz 55
48143 Münster - Germany

Tel: ++49 251 8324791
Fax: ++49 251 8328371
Web: http://www.fufezan.net

On Aug 11, 2008, at 20:33 , Justin A. Lemkul wrote:

>
>
> Christian Fufezan wrote:
>> Dear gmx users,
>> I am new to MD and working my way through some tutorials. I saw  
>> that pdb2gmx has the "-inter" flag which is used to specify which  
>> conformers/protonation stats should be used.
>> Is there a way in which this can be automatised ?
>> For example, lets say I have a list.txt
>> ....
>> HIS A 105 -> HISB
>> ....
>> and I would like to use that list for all runs to be used.
>
> Would this be useful:
>
> http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive
>
> Trying to automate this procedure using -inter is probably a lot  
> more work than actually interacting with pdb2gmx.  If you're happy  
> with the default protonation states of all the other titratable  
> sites (check pdb2gmx -h), then you can use -his instead, which might  
> de-complicate things.  Otherwise, you have to know the order of all  
> the interactively selected residues, which protonation state to give  
> them, and how many of each you have.
>
> -Justin
>
>> Thanks in Advance
>> Christian Fufezan
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before  
>> posting!
>> Please don't post (un)subscribe requests to the list. Use thewww  
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the www  
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php