Hi Pengfei,
Thank you for the generous suggestions.
Which version of AmberTools did you use?
16
Did you use MCPB.py to parameterize the metal site?
I used MCPB.py only to extract the force constants from gaussian
calculation and edited the frcmod file that I generated with
antechamber/parmchk.
I think the problem was in creating RU library.
I will rebuild the library again.
Thank you very much,
Sanaa
On Thu, Oct 12, 2017 at 8:47 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Sanaa,
>
> Which version of AmberTools did you use? Did you use MCPB.py to
> parameterize the metal site?
>
> If you want to parameterize the Ru complex with a bonded model, in the
> supporting information (SI) of the MCPB.py paper:
> http://pubs.acs.org/doi/suppl/10.1021/acs.jcim.5b00674 <
> http://pubs.acs.org/doi/suppl/10.1021/acs.jcim.5b00674>, there are two
> examples. The second example is about an organic metal complex of Os2+,
> there are both instructions and modeling files in the SI (PDF + ZIP). An Ru
> complex can be parameterized in a similar way.
>
> If you want to just use a nonbonded model for the Ru ion, you can check
> the following example:
>
> >>Ru.cmd
> i = createAtom RU Ru2+ 2.0
> set i element "Ru"
> set i position { 0 0 0 }
> r = createResidue RU
> add r i
> RU = createUnit RU
> add RU r
> saveOff RU ./Ru.lib
>
> >>Ru.pdb
> HETATM 1 RU RU A 1 43.000 48.903 6.560 1.00 47.48
>
> >>Ru.frcmod
> Remarks goes here
> MASS
> Ru2+ 101.07
>
> NONBON
> Ru2+ 1.4815 0.056 !Adopted from atom type Ru6+2 from UFF (Rappe et al.
> JACS, 114, 10024)
>
> >>tleap.in
> loadoff Ru.lib
> loadamberparams Ru.frcmod
> mol = loadpdb Ru.pdb
> saveamberparm mol Ru.prmtop Ru.inpcrd
> quit
>
> You can perform “tleap -s -f Ru.cmd > Ru.out” to generate the Ru.lib file,
> and then use “tleap -s -f tleap.in > tleap.out” to generate the Ru.prmtop
> and Ru.inpcrd files.
>
> Hope it helps,
> Pengfei
>
>
> > On Oct 12, 2017, at 11:56 AM, Sanaa ALAbbad <salabbad79.gmail.com
> <mailto:salabbad79.gmail.com>> wrote:
> >
> > Szymon,
> >
> > Thanks.
> > Yes I did, and included all coordination parameters, force field, and
> > charges in frcmod and mol2 files. But I am wondering since I found these
> > errors if there are other errors too?
> >
> > Sanaa
> >
> > On Thu, Oct 12, 2017 at 10:51 AM, Szymon Żaczek <szymonzaczek.gmail.com
> <mailto:szymonzaczek.gmail.com>>
> > wrote:
> >
> >> Dear Sanaa,
> >>
> >> have you considered using MCPB.py? It is a very robust and versatile
> >> tool implemented in AmberTools for obtaining force field parameters
> >> for metal ions. More info may be found in tutorial:
> >> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm> or in a
> >> paper by Li and Merz (DOI: 10.1021/acs.jcim.5b00674).
> >>
> >> Kind regards,
> >> Szymon Zaczek
> >>
> >> 2017-10-12 17:27 GMT+02:00 Sanaa ALAbbad <salabbad79.gmail.com <mailto:
> salabbad79.gmail.com>>:
> >>> Dear Ambers,
> >>>
> >>> I defined Ru in the atomic_ions.cmd then with tleap created the
> library.
> >>> The complex included 98 atoms.
> >>> Then I generated inpcrd and prmtop.
> >>> I manually corrected the following in the prmtop:
> >>>
> >>> 1- tleap wrote the Ru atomic_number =-1 ! so I corrected to 44
> >>> 2- tleap assigned only 2 atoms for the complex in the
> >> (ATOMS_PER_MOLECULE)
> >>> section.
> >>> 3- I corrected the SOLVENT_POINTERS section too.
> >>>
> >>> The simulation went fine but destroyed the complex!!
> >>>
> >>> I checked the validity of the topology file and the error is
> ParmWarning:
> >>> ATOMS_PER_MOLECULE section corrupt! Molecules are not contiguous!
> >>> Is this error what cause this problem in the minimization?
> >>> in other words
> >>> Is there other parameters that I am not aware of that have to be
> >> corrected
> >>> in the topology files?
> >>>
> >>> Thanks for any help,
> >>>
> >>> Sanaa Al Abbad
> >>> _______________________________________________
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> >>
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Received on Fri Oct 13 2017 - 06:30:02 PDT
