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 Thu Oct 12 2017 - 20:00:02 PDT
