Dear all
I am trying to perform MMPBSA calculations for a docked complex (by using
MMPBSA.PY). My protein contains Na+ ions along with Mg2+. I tried to load
the Na+ ions by using all the force field parameters available for
monovalent ions but all the time i received the error.
I have used the following for adding IONS in AMBER14.
*> loadamberparams frcmod.ionslrcm_hfe_tip3p*
*> loadamberparams frcmod.ions1lsm_iod *
*> loadoff ions94.lib*
*>saveamberparm pro protein.top protein.crd*
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<Na+ 264>.A<Na+ 1> Could not find vdW (or other) parameters for
type: IP
For atom: .R<Na+ 265>.A<Na+ 1> Could not find vdW (or other) parameters for
type: IP
For atom: .R<Na+ 266>.A<Na+ 1> Could not find vdW (or other) parameters for
type: IP
For atom: .R<Na+ 267>.A<Na+ 1> Could not find vdW (or other) parameters for
type: IP
For atom: .R<Na+ 268>.A<Na+ 1> Could not find vdW (or other) parameters for
type: IP
For atom: .R<Na+ 269>.A<Na+ 1> Could not find vdW (or other) parameters for
type: IP
For atom: .R<Na+ 270>.A<Na+ 1> Could not find vdW (or other) parameters for
type: IP
*Parameter file was not saved.*
I have already tried all the possible solutions given on mailing list. I am
unable to put my finger on the actual problem.
Please help me out.
Many Thanks
Sumra Wajid Abbasi
PhD Scholar
Computational Biology Lab, National Center for Bioinformatics
Quaid-e-Azam University, Islamabad-45320 Pakistan.
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Received on Thu Nov 12 2015 - 01:00:04 PST
