Dear Amber users,
I want to simulate a zinc metalloprotease and have determined the metal site parameters using MCPB.py
After tleap I ran the prmtop through cpptraj and got the following error:
Error: Atom 12495 was assigned a lower molecule # than previous atom. This can
Error: happen if 1) bond information is incorrect or missing, or 2) if the
Error: atom numbering in molecules is not sequential. If topology did not
Error: originally contain bond info, 1) can potentially be fixed by
Error: increasing the bondsearch cutoff offset (currently 0.200). 2) can be
Error: fixed by either using the 'fixatomorder' command, or using
Error: the 'setMolecules' command in parmed.py.
Error: Could not determine molecule information for editnoLINK_bondhash_CLedit_NDOM_CPLX_Neut_Sol.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for editnoLINK_bondhash_CLedit_NDOM_CPLX_Neut_Sol.prmtop.
Using setMolecules in parmed.py gave a new prmtop with no errors in cpptraj.
Running parmed and checkValidity on the new prmtop gave the following warning:
> checkValidity
Determining validity of prmtop
1 total warnings
NonUniversalWarning: Modified off-diagonal LJ parameters detected
I have not changed the LJ parameters in parmed.
Jason Swails mentioned in a previous post (Curious behavior of cpptraj in ambertools 13.1):
> Hmm... I wonder why this warning was triggered. Unless you used "changeLJPair" in ParmEd (or somehow otherwise manually changed the LENNARD_JONES_ACOEF or BCOEF elements of the topology file, this should not be an issue.
I noticed that the previous post was also about a protein coordinated to zinc. Does the new parameters derived from mcpb.py somehow trigger this warning?
Should I worry about it or can I use the prmtop and rst7 for minimization?
Kind regards
Lizelle Lubbe
PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Tue Jul 11 2017 - 08:30:03 PDT
