You could grep IP from the parameter files to see which ones define it,
which might give a clue.
Bill
On 11/12/15 12:44 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 wrote:
> 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 - 02:00:03 PST
