Hi,
Thank you so much for the suggestions.
I checked the prmtop files that I created with the corresponding
inpcrd files and looked very fine in VMD. However when I am creating
the snapshots usinf extract_coord.mmpbsa, the crd files of the lig and
com are showing irregular bondings. I read a similar problem in
http://archive.ambermd.org/201103/0529.html.
Plz tell me is there any other way to generate snapshots for mmpbsa calculation.
Also as you suggested, when I am running MMPBSA.py, the following
errors are apperaing:
Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
modified Bondi radii (mbondi)
Preparing trajectories with ptraj...
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
5 frames were read in and processed by ptraj for use in calculation.
Starting sander calls
Starting gb calculation...
bad atom type: K
bad atom type: K
Starting pb calculation...
Cannot match namelist object name cutcap
namelist read: misplaced = sign
Cannot match namelist object name 1
Cannot match namelist object name xcap
namelist read: misplaced = sign
Cannot match namelist object name ycap
namelist read: misplaced = sign
Cannot match namelist object name zcap
namelist read: misplaced = sign
namelist not terminated with / or &end
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Cannot match namelist object name cutcap
namelist read: misplaced = sign
Cannot match namelist object name 1
Cannot match namelist object name xcap
namelist read: misplaced = sign
Cannot match namelist object name ycap
namelist read: misplaced = sign
Cannot match namelist object name zcap
namelist read: misplaced = sign
namelist not terminated with / or &end
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Cannot match namelist object name cutcap
namelist read: misplaced = sign
Cannot match namelist object name 1
Cannot match namelist object name xcap
namelist read: misplaced = sign
Cannot match namelist object name ycap
namelist read: misplaced = sign
Cannot match namelist object name zcap
namelist read: misplaced = sign
namelist not terminated with / or &end
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Bad data for namelist object igb
Bad data for namelist object igb
namelist read: misplaced = sign
Error: No potential terms in sander output! Check output files.
NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
Kindly help
On 12/27/13, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Dec 26, 2013 at 8:37 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
>
>> Hi,
>>
>> I checked and found that the bond energies are missing in all the
>> frames in snapshot_lig.all.out and also for snapshot_com.all.out
>> (while snapshot_rec.all.out has bond energy in all the frames).
>>
>
> Something seems to be wrong with the topology file(s) and or their
> compatibility with the input trajectories (that is usually what happens
> when the energies are all *'s, especially bond energies).
>
>
>> So I checked the lig_vac.prmtop, com_vac.prmtop and rec_vac.prmtop and
>> found that the pdb structures formed by the above were fine (used
>> ambpdb command).
>>
>
> You should visualize the topology files with some of the structures
> generated by mm_pbsa.pl and look for any irregularities. Other than that
> very general advice, I will really only be able to provide help with
> MMPBSA.py, so I suggest that you try using that version instead.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Asfa Ali
Prof. S. Bhattacharya's group,
Dept. of Organic Chemistry,
Indian Institute of Science,
Bangalore-12
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Dec 28 2013 - 02:00:03 PST
