On Tue, Dec 13, 2016 at 11:07 AM, Sowmya Indrakumar <soemya.kemi.dtu.dk>
wrote:
> Dear All,
> I could now figure out how to do this using explicit solvent:
> important points to note:
>
> 1) while saving the topology files, *saveAmberParm* should be mentioned
> instead of *saveamberparm*, otherwise the topology files will not generated
> with leaprc.constph.
>
tleap is case-insensitive, so saveAmberParm and saveamberparm are the same.
>
> 2) running : cpinutil.py -p *.parm7 -igb 2 -o *.cpin -op *.modO.parm7
> -resnames AS4 GL4 HIP CYS
> will give the below mentioned error:
> Traceback (most recent call last):
> File "/opt/amber16/bin/cpinutil.py", line 294, in <module>
> main(opt)
> File "/opt/amber16/bin/cpinutil.py", line 264, in main
> parm.writeParm(opt.outparm)
> AttributeError: 'AmberParm' object has no attribute 'writeParm'
>
This indicates your Amber installation is out-of-date. This is a bug that
was fixed in June via update 3 for AmberTools 16.
I would suggest re-running configure and reinstalling AmberTools to make
sure you bring in all of the updates.
HTH,
Jason
--
Jason M. Swails
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Received on Tue Dec 13 2016 - 10:00:03 PST
