The former email is for MCPB.py.
I would recommend to use MCPB.py instead of MCPB since the former is much more user-friendly than the later and the later one is not under development any more.
> On Oct 18, 2017, at 11:19 AM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> Hi Sanaa,
>
> You can use the “add_bonded_pairs” variable to solve the problem:
>
> Please see Page 296-297 in http://ambermd.org/doc12/Amber17.pdf <http://ambermd.org/doc12/Amber17.pdf>.
>
> Note that there is a typo in the example of the manual (in the top of Page 297), which should be:
>
> "add_bonded_pairs 1001-1320 1001-1380”
>
> In which the bonded pairs should be connected by the dash symbol.
>
> Kind regards,
> Pengfei
>
>> On Oct 17, 2017, at 6:10 PM, Sanaa ALAbbad <salabbad79.gmail.com <mailto:salabbad79.gmail.com>> wrote:
>>
>> Hi AMBERs,
>>
>> I am trying to create bonds between Ru and the ligands.(bipyridine, two
>> PPh3, CO, and hydride). when I followed the Os example of using MCPB, it is
>> only identified the Ru-bipyridine bonds.
>>
>> So I tried to use genMetalFF.sh. following the steps in the link
>> http://ambermd.org/tutorials/advanced/tutorial20/mcpb.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpb.htm>
>> for each ligand I searched for the library that will represent each atom
>> type.
>> I will give the phosphorous as example of what I have done:
>>
>> 1- in the pdb file there are 2 atoms
>> ATOM 3 P PPA A 3 -0.992 -0.027 -2.444 0.00
>> 0.00 P
>> ATOM 4 P PPA A 4 -0.995 -0.021 2.440 0.00
>> 0.00 P
>>
>> 2- in the script I edited it as
>>
>>> copyStdResidue terminal/PPA NAME/PP1
>>> copyStdResidue terminal/PPA NAME/PP2
>> #####
>>> copyAtomType parm_gaff/p5 NAME/P1
>>> copyAtomType parm_gaff/p5 NAME/P2
>> ####
>>> setAtomType NAME/PP1/...P NAME/P1
>>> setAtomType NAME/PP2/...P NAME/P2
>> ####
>>
>> the error:
>> Incorrect use of setAtomType: Can't find stdAtom: P
>>
>> Any idea?
>>
>> Thank
>> Sanaa AlAbbad
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Oct 18 2017 - 09:30:02 PDT
