Ping,
You need to do this *in* xleap/tleap/sleap, not from the command
line. As Jason suggested, you should read the AmberTools manual or at
least do one of the basic AMBER tutorials (
http://ambermd.org/
tutorials/) -- there are several examples of these types of actions
there.
Paul
On Jul 1, 2010, at 11:37 AM, Ping wrote:
> Hi Bill,
>
> [xiuchen.sw2123-06 leap]$ loadpdb
> /home/xiuchen/Desktop/protonatedsingleprotein.pdb
> loadpdb: Command not found.
> [xiuchen.sw2123-06 leap]$
>
> do you know what is the problem?
>
> Thanks!
>
> On Thu, Jul 1, 2010 at 1:19 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>>> Hi Bill, do I need to add the pdb file name of the protein with 19
>>> H+ in
>>> the command "addions my_mol Cl- 0"?
>>
>> leap> my_mol = loadpdb my_mol.pdb
>> leap> addions my_mol Cl- 0
>>
>> 'my_mol' can be whatever string works for you.
>>
>> Bill
>>
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>>
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Received on Thu Jul 01 2010 - 12:00:04 PDT
