Great, your fix seems to have worked, thanks a lot for your help.
Thanks,
Rohith Mohan
BioMoDeL
UC Riverside
Ph.D. Graduate Student
On Thu, Jul 30, 2015 at 1:53 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> On Thu, Jul 30, 2015 at 4:06 PM, Rohith Mohan <rmoha004.ucr.edu> wrote:
>
>> I didn't see a warning about ATOMS_PER_MOLECULE so I think the PSF and
>> Amber files should be compatible. I generated a chamber-free topology using
>> cpptraj and visualizing in VMD still resulted in a warped image.
>>
>> While comparing the coordinates from the inpcrd file and the NAMD PDB
>> file I noticed that for several coordinates there was a mismatch in the
>> sign of a coordinate. For example, -23.667 -13.159-150.455 from the PDB
>> becomes -23.6670000 -13.1590000 150.4550000. -150.455 becomes 150.455 which
>> results in the structure being warped I believe. Additionally in some cases
>> there's a lack of space between coordinates so I wonder if that may
>> affecting the structure as well when AMBER reads it
>> e.g: -95.272-102.260-121.094 from the PDB becomes -95.2720000-102.2600000
>> 121.0940000 in the .inpcrd file.
>>
>
> Yep, I can confirm this. The problem is that the PDB parser skipped the
> first character in the Z-coordinate field. I never saw it before because
> 99.9% of all Z-coordinates in PDB files are 7 fields or fewer, so it
> usually just skipped whitespace. In your case, it neglected a negative
> sign and completely wrecked the resulting inpcrd file.
>
> Luckily the fix is exceedingly easy -- I will make an update for
> AmberTools 15 shortly. In the meantime, you can make the fix by hand. Go
> to the file $AMBERHOME/AmberTools/src/parmed/chemistry/formats/pdb.py and
> look for line 194. It should read:
>
> x, y, z = line[30:38], line[38:46], line[47:54]
>
> Change the 47 to a 46 and make sure you recompile. To do this just for
> ParmEd, you can go to $AMBERHOME/AmberTools/src/parmed and type:
>
> python setup.py install --prefix=$AMBERHOME
>
> Thanks for the report, and let me know if you still have problems,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Fri Jul 31 2015 - 14:00:04 PDT
