Hi,
I am running nmode calculations (Amber11, python script, serial version) on
a complex with ~500atoms. I get the following results:
ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:
Complex:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: -1.0000 0.0000
Rotational: -1.0000 0.0000
Vibrational: -1.0000 0.0000
Total: -1.0000 0.0000
Receptor:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: -1.0000 0.0000
Rotational: -1.0000 0.0000
Vibrational: -1.0000 0.0000
Total: -1.0000 0.0000
Ligand:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: -1.0000 0.0000
Rotational: -1.0000 0.0000
Vibrational: -1.0000 0.0000
Total: -1.0000 0.0000
DELTA S total= 1.0000 +/- 0.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
WARNINGS:
Not all of your snapshots minimized within tolerable limits for nmode
The MMPBSA_complex_nm.out, _MMPBSA_receptor_nm.out, or _MMPBSA_ligand_nm.out
files end abruptly without error. They end with
Root-mean-square gradient of input coords is 0.244797413344676
This is greater than the requested maximum: 1.000000000000000E-003
My input file is:
&general
endframe=50000000000, verbose=1, initial_traj=1,
/
&nmode
nmstartframe=1, nmendframe=7200,
nminterval=720,
maxcyc=50000, drms=0.0001,
/
I would be really grateful if anyone could help me troubleshoot the issue. I
am sure memory is not an issue since I am using 12GB for my system with
about 500 atoms. The snapshots I am using are from post 5ns MD.
Thanks
Amit
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Received on Fri Mar 25 2011 - 11:30:03 PDT
