What you need to do is add the radius of Cl atom in the mdread.f file and
then re install or recompile tje amber version which you have. I ALSO had
faced the same situation , and it worked well for me after following the
above step
On 24 Jul 2013 21:28, <sribone.fcq.unc.edu.ar> wrote:
> Dear all, Im running MMPBSA.py for a receptor-ligand system where the
> ligand has a chloride atom in its structure. When I run the MMPBSA.py a
> received the mesage: 'bad atom type: cl'. I already search for the solution
> in the amber mailing list and found that I need to add the chloride radius
> to the mdread.f90, so I did it manually but it didn't work.
> I also read an example to do it as a patch
> (http://archive.ambermd.org/201101/0220.html.) for a Na+ atom, but I don't
> understand how I can apply it for my chloride atom. Can anyone help me to
> make this patch or explain me how can I make it.
> Thank you very much in advance for your help.
> Regards,
>
> Sergio Ribone.
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>
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Received on Wed Jul 24 2013 - 09:30:02 PDT
