Hello Abhi,
It seems this error comes from that in your PDB file there are two atoms have the same name inside a certain residue, which caused MCPB.py has recognition problem. The way to solve the problem is to modify the PDB file (just changing the atom name(s) without changing the sequence of the atoms) and run MCPB.py from step 1 (Gaussian/GAMESS-US calculations are not needed to be performed again, the old log file could be used directly).
Kind regards,
Pengfei
> On Nov 20, 2016, at 12:34 AM, Abhi Acharya <abhi117acharya.gmail.com> wrote:
>
> Hello Dr. Pengfei.
>
> I made the suggested changes to the code. However, this time I am getting a
> different error saying that the charges and atoms do not match.
>
> Here is the output:
>
> The input file you are using is : 3UJO.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> The following is the input variable you have:
> The variable ion_ids is : [3825, 3826]
> The variable ion_info is : []
> The variable ion_mol2files is : ['CA.mol2', 'CU.mol2']
> The variable original_pdb is : 3UJO_fixed_H.pdb
> The variable add_bonded_pairs is : []
> The variable additional_resids is : []
> The variable anglefc_avg is : 0
> The variable bondfc_avg is : 0
> The variable cut_off is : 2.8
> The variable chgfix_resids is : []
> The variable force_field is : ff14SB
> The variable frcmodfs is : []
> The variable gaff is : 1
> The variable group_name is : 3UJO
> The variable ion_paraset is : CM (Only for nonbonded model)
> The variable large_opt is : 1
> The variable lgmodel_chg is : -99
> -99 means program will assign a charge automatically.
> The variable naa_mol2files is : ['WAT.mol2']
> The variable scale_factor is : 1.0
> ATTENTION: This is the scale factor of frequency. The
> force constants will be scaled by multiplying the square
> of scale_factor.
> The variable smmodel_chg is : -99
> -99 means program will assign a charge automatically.
> The variable software_version is : gms
> The variable sqm_opt is : 0
> The variable water_model is : TIP3P
> ******************************************************************
> * *
> *======================RESP Charge fitting=======================*
> * *
> ******************************************************************
> ***Generating the 1st stage resp charge fitting input file...
> ***Generating the 2nd stage resp charge fitting input file...
> ***Doing the RESP charge fiting...
> CAUTION: THE VDW RADIUS OF ATOMIC NUMBER 20IS UNKNOWN AND HAS
> BEEN SET TO1.80 ANGSTROMS IN THE GAMESS CALCULATION.
> CAUTION: THE VDW RADIUS OF ATOMIC NUMBER 29IS UNKNOWN AND HAS
> BEEN SET TO1.80 ANGSTROMS IN THE GAMESS CALCULATION.
> =========================Checking models==========================
> ***Check the large model...
> Good. The charges and atom numbers are match for the large model.
> Good. There are 186 atoms in the large model.
> ***Check the standard model...
> Traceback (most recent call last):
> File "/home/bp-lab/install-fold/amber16/bin/MCPB.py", line 600, in
> <module>
> premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
> File
> "/home/bp-lab/install-fold/amber16/lib/python2.7/site-packages/mcpb/resp_fitting.py",
> line 517, in resp_fitting
> raise pymsmtError('Error: the charges and atom numbers are mismatch '
> pymsmtexp.pymsmtError: Error: the charges and atom numbers are mismatch for
> the standard model!
>
> Kindly help.
>
> Best Regards,
> Abhishek
>
> On Wed, Nov 16, 2016 at 4:15 PM, Abhi Acharya <abhi117acharya.gmail.com>
> wrote:
>
>> Hello Amber users,
>>
>> Perhaps my question was not clear previously.
>>
>> I have been trying to calculate charges for active site metal ions and the
>> coordinating residues using the seminario method. i follow the tutorial by
>> Pengfei et al.
>>
>> These are the steps I followed:
>>
>> 1. created the pdb for the protein model with Hydrogens added. Also
>> created the mol2 files for active site water molecules (single file with 4
>> molecules) and ions (one each for Cu and Ca ion).
>> 2. Next I proceeded to generate the small and large active site models
>> using GAMESS.
>> 3. Performed geometry optimization and fc calculation for small model.
>> Optimized the large model and performed charge calculations using GAMESS.
>> 4. Generated the frcmod file for the active site using the command:
>> MCPB.py -i input.in -s 2
>>
>> So far so good. My problem is the following:
>> A. How to proceed after creating the initial frcmod file i.e after the
>> second step MCPB.py -i input -s 2. Everything works smoothly till this
>> step. However, in the next step:
>>
>> MCPB.py -i input -s 3
>>
>> I get the following error:
>> The following is the input variable you have:
>> The variable ion_ids is : [3825, 3826]
>> The variable ion_info is : []
>> The variable ion_mol2files is : ['CA.mol2', 'CU.mol2']
>> The variable original_pdb is : 3UJO_fixed_H.pdb
>> The variable add_bonded_pairs is : []
>> The variable additional_resids is : []
>> The variable anglefc_avg is : 0
>> The variable bondfc_avg is : 0
>> The variable cut_off is : 2.8
>> The variable chgfix_resids is : []
>> The variable force_field is : ff14SB
>> The variable frcmodfs is : []
>> The variable gaff is : 1
>> The variable group_name is : 3UJO
>> The variable ion_paraset is : CM (Only for nonbonded model)
>> The variable large_opt is : 1
>> The variable lgmodel_chg is : -99
>> -99 means program will assign a charge automatically.
>> The variable naa_mol2files is : ['WAT.mol2']
>> The variable scale_factor is : 1.0
>> ATTENTION: This is the scale factor of frequency. The
>> force constants will be scaled by multiplying the square
>> of scale_factor.
>> The variable smmodel_chg is : -99
>> -99 means program will assign a charge automatically.
>> The variable software_version is : gms
>> The variable sqm_opt is : 0
>> The variable water_model is : TIP3P
>> ******************************************************************
>> * *
>> *======================RESP Charge fitting=======================*
>> * *
>> ******************************************************************
>> ***Generating the 1st stage resp charge fitting input file...
>> ***Generating the 2nd stage resp charge fitting input file...
>> ***Doing the RESP charge fiting...
>> Traceback (most recent call last):
>> File "/home/bp-lab/install-fold/amber16/bin/MCPB.py", line 600, in
>> <module>
>> premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
>> File "/home/bp-lab/install-fold/amber16/lib/python2.7/site-
>> packages/mcpb/resp_fitting.py", line 443, in resp_fitting
>> get_esp_from_gms(mklogf, espf)
>> File "/home/bp-lab/install-fold/amber16/lib/python2.7/site-packages/msmtmol/gmsio.py",
>> line 222, in get_esp_from_gms
>> for i in range(bln, eln+1):
>> UnboundLocalError: local variable 'eln' referenced before assignment
>>
>>
>> B. I did not find any mol2 files generated for the active site
>> coordinating residues. Perhaps, these files will be generated if the above
>> errors are rectified.
>> Am I correct?
>>
>>
>> Kindly help.
>>
>>
>> Thanks and Regards,
>> Abhishek Acharya
>>
>> On Sat, Nov 12, 2016 at 2:39 PM, Abhi Acharya <abhi117acharya.gmail.com>
>> wrote:
>>
>>> Hi amber users,
>>>
>>> I am trying to use the MCPB.py workflow to derive parameters for an
>>> active site containing Cu2+ and Ca2+ ions. The Cu2+ ion is coordinated by
>>> two water molecules, and active site residues Asp, His etc.
>>> My question is that in the input file for MCPB.py do we need to specify
>>> separate mol2 files for the two water molecules and the coordinating
>>> residues? In the MCPB.py tutorial at this link:
>>> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm the input
>>> file does not specify any of the coordinating His residues. But still in
>>> the 3rd step i.e. MCPB.py -i 1OKL.in -s 3, the tutorial says that mol2
>>> files for HD1, HD2 and HE1 will be created. I am a bit confused.
>>>
>>> I request you to kindly clarify this.
>>>
>>> Thanks and Regards,
>>> Abhishek Acharya
>>> CFTRI, Mysore.
>>>
>>
>>
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Received on Mon Nov 21 2016 - 14:30:02 PST
