[gmx-users] pdb2gmx -inter automatised ?

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 11 20:33:05 CEST 2008

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:


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.


> Thanks in Advance
> Christian Fufezan
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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