I solved the problem. The extension of the output file was .out changed to
.log and worked.
Thanks!
Sanaa
On Wed, Oct 18, 2017 at 6:14 PM, Sanaa ALAbbad <salabbad79.gmail.com> wrote:
> 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
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 19 2017 - 07:00:04 PDT
