Hi Lizelle,
As Shahid suggested, the error may be related to your quantum software version you used. Try to add “software_version g09” as an independent line into your MCPB.py input file to see whether it works.
"The tutorial mentions that you should confirm that coordination bonds do not break. How do I check for this?”
For this question, do you know how to use GaussView? If so, you can check whether the coordination bonds break or not by using that visualization software and your eyes.
Kind regards,
Pengfei
> On Jul 4, 2017, at 9:25 AM, Dr. M. Shahid <mohammad.shahid.gmail.com> wrote:
>
> Hi,
>
> your input file points to the g03 version but you said you used g09?
> Also you can try step 2e or 2z if that fits for your Zn system..
>
> Best regards,
>
> --
> Shahid.
>
>
>
> On Tue, Jul 4, 2017 at 1:05 PM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
>
>> Dear Amber users,
>>
>> I am trying to parameterize Zn coordinated to HID, HID, GLU and a water
>> molecule and have been following the AMBER advanced tutorial 20 on MCPB.py.
>>
>> The sidechain model geometry was optimized, force constants calculated for
>> the large model and the sidechain model fchk file generated.
>> Next, the Merz-Kollman RESP charge calculation was done followed by the
>> Gaussian 09 bug fix and espgen in AMBER.
>>
>> The tutorial mentions that you should confirm that coordination bonds do
>> not break. How do I check for this?
>>
>> In the final modelling step using the gaussian output I get the following
>> error:
>>
>> [llubbe.login2 04072017_MCPBpycontd]$ MCPB.py -i 03072017_NDOM.in -s 2
>>
>>
>>
>> ******************************************************************
>> * Welcome to use MCPB.py program *
>> * Author: Pengfei Li *
>> * Merz Research Group *
>> * Michigan State University *
>> * All Rights Reserved *
>> ******************************************************************
>>
>>
>>
>> The input file you are using is : 03072017_NDOM.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>> The following is the input variable you have:
>> The variable original_pdb is : 03072017_NDOM_H_All_renum.pdb
>> The variable ion_ids is : [9749]
>> The variable ion_mol2files is : ['ZN_renum.mol2']
>> The variable group_name is : NDOM
>> The variable cut_off is : 2.8
>> The variable ionchg_fixation is : 0
>> The variable gau_version is : g03
>> The variable sqm_opt is : 0
>> The variable force_field is : ff14SB
>> The variable gaff is : 1
>> The variable frcmodfs is : []
>> The variable naa_mol2files is : ['WAT.mol2']
>> The variable water_model is : TIP3P
>> The variable ion_paraset is : CM (Only for nonbonded model)
>> The variable ion_info is : []
>> ******************************************************************
>> * *
>> *===================Generate the Initial frcmod file=============*
>> * *
>> ******************************************************************
>> Atoms which has changed the atom types: [5694, 5750, 6151, 9749, 9750]
>> 361-HID.5694-NE2 : NB --> X1
>> 365-HID.5750-NE2 : NB --> X2
>> 389-GLU.6151-OE1 : O2 --> X3
>> 613-ZN.9749-ZN : ZN --> Z1
>> 614-WAT.9750-O : OW --> X4
>> ==================Using the Seminario method to solve the problem.
>> Traceback (most recent call last):
>> File "/apps/chpc/chem/amber/14/bin/MCPB.py", line 434, in <module>
>> g0x)
>> File "/apps/chpc/chem/amber/14/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py",
>> line 306, in gene_by_QM_fitting_sem
>> 'Int Atom Types')
>> File "/apps/chpc/chem/amber/14/lib/python2.7/site-packages/pymsmtmol/gauio.py",
>> line 47, in get_crds_from_fchk
>> crds.append(float(j))
>> ValueError: could not convert string to float: Force
>>
>> Any advice on how to solve this would be greatly appreciated!
>>
>> Kind regards
>>
>> Lizelle Lubbe
>>
>> PhD (Medical biochemistry) candidate
>> Department of Integrative Biomedical Sciences
>> University of Cape Town
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Received on Wed Jul 05 2017 - 20:30:03 PDT
