Thank you very much for your help.
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Jul 24 2013 - 10:30:08 PDT
