Dear Prof.Li,
Thank you for clarifying this issue. I did build the bonds fine. But when
running MCPB.py -i Rudcbp.in -s 3 the error:
Traceback (most recent call last):
File "/usr/local/amber16/bin/MCPB.py", line 600, in <module>
premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
File
"/usr/local/amber16/lib/python2.7/site-packages/mcpb/resp_fitting.py", line
441, in resp_fitting
get_esp_from_gau(mklogf, espf)
File "/usr/local/amber16/lib/python2.7/site-packages/msmtmol/gauio.py",
line 491, in get_esp_from_gau
crd = (float(line[32:42])/B_TO_A, float(line[42:52])/B_TO_A,
float(line[52:62])/B_TO_A)
ValueError: could not convert string to float: **********
In the Ru.mol2 files I defined the Ru charge 2+ and in RES.mol2 file I
defined the hydride charge to be -1. So that created the right charge and
multiplicity for small and large model (1 1).
I noticed that in the Os files the g03 has been used while I am using g09
so the output format is slightly different. I know in the script it should
read any g0x but I am not sure why it cannot fit the RESP charge.
I deeply appreciate your help with this regard.
Best,
Sanaa AlAbbad
On Wed, Oct 18, 2017 at 10:21 AM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> 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
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Wed Oct 18 2017 - 17:30:02 PDT
