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 Sat Nov 19 2016 - 23:00:04 PST
