searching software to add hydrogens to a pdb file

[lordy99]

some docking software require added hydrogens to the given pdb file (sometimes polar only and sometime all) . does anyone know a software which can do that in a correct way (now i am using autodock tools but for example x-score complains that the hydrogens where not added correctly)
in the ideal case the software is console based which would allow an automation

thx
lordy

[ecualchem]

You can probe with DeepView/Swiss-PdbViewer 3.7 you can see the link in expasy (I can´t still to put links since I have posted 15 responses )

Use a St. Google please, it is the better master for the urgences, but with patience, sometimes I was desperated too.

I can see that have the option that you need.

Enjoy your time .I can´t enought time to stydy the software. Can you sendme a message if was good for you.

Best regards from Ecuador

Giordano

[lordy99]

Originally Posted by ecualchem

You can probe with DeepView/Swiss-PdbViewer 3.7 you can see the link in expasy (I can´t still to put links since I have posted 15 responses )

Use a St. Google please, it is the better master for the urgences, but with patience, sometimes I was desperated too.

I can see that have the option that you need.

Enjoy your time .I can´t enought time to stydy the software. Can you sendme a message if was good for you.

Best regards from Ecuador

Giordano

currently i have some technical difficulties with deepview "can not open rotolib.aa" on unix but i am going to fix that tomorrow. then i can give you some feedback

[molecule2005]

Great! very helpful tips guys

[ecualchem]

OK a pleasure to help you

Are you study bioinformatics too?

Where ?

At the moment , I m seeking a training program (presential, I need touch the bioinformatics in vivo with a team) for apply for the next year , I hope to finish my second year ( a investigation work ) in this year and beginning my career with a better training that I can get.
Yes, I can improve my level of speaking and graammar english level.

Best regards and enyoy your tool, bioinformatics is a greatest a marvelous world , I love it, but in Ecuador I can´t resources for this way.

[lordy99]

Originally Posted by ecualchem

DeepView

deepview seems to be a nice program and it can add hydrogen as wanted but the problem remains because the inculded scripting language does not support the add hydrogen command. so i would have to add them by hand each time which is not really satisfying. i am searching for something which can be used in the following way:

addHydrogens sourcefile.pdb outputfile.pdb flagIfOnlyPolarOnes

and it should be runable under linux (fedora6 zod)

[lordy99]

so now guys and girls here is the solution

open babel [1] is able to do all the things i wanted via command line

babel -h p.pdb p.mol2 //or whatever you like




[1] h_t_t_p://openbabel.sourceforge.net/wiki/Main_Page //crap i still cant post links

[ecualchem]

Congratlations and thaks for the link it is good to know that a similar open source program exist. I believe that you will be write about this problem to Swiss_PDBViewer . I think that will be a version for linux but if don´t exist .
This is the new project for somebody .

Best Regards

[admin]

Awesome!

great work guys