Re: [AMBER] Problem in protonating.

From: Jason Swails <>
Date: Fri, 13 Mar 2015 08:14:42 -0400

On Fri, 2015-03-13 at 16:46 +0530, Harshala Haldankar wrote:
> Hi,
> I am new to Amber software and want to simulate a* helical peptide *in
> water. I am trying to protonate my peptide in xleap using following command:

What do you mean "protonate" your peptide? You're just trying to add
protons that are not present in your PDB file? Or are you trying to add
protons to titratable groups, like carboxylates? In both of these
cases, tleap will add hydrogen atoms for you (and "reduce" can be used
to put them in perhaps better positions).

> protonate -k -d $AMBERHOME/dat/PROTON_INFO -i pcpep_cap1.pdb -o pc_prot.pdb
> -l pcprot.out
> and i tried this also
> $AMBERHOME/exe/protonate -k -d $AMBERHOME/dat/PROTON_INFO -i pcpep_cap1.pdb
> -o pc_prot.pdb -l pcprot.out

What version of Amber are you using?? $AMBERHOME/exe has not been a
directory in the distribution for many years. You should upgrade to
AmberTools 14, available free on the Amber website.

> but am getting syntax error.

It is always better to show exact output.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 13 2015 - 05:30:02 PDT
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