Date: Sat, 29 Mar 2025 08:51:59 +0530
Hey, thanks for replying
The problem is solved.
Thanks and regards
Dipankar
On Sat, Mar 29, 2025, 8:39 AM Li, Zhen <lizhen6.chemistry.msu.edu> wrote:
> Hi Dipankar,
>
> Yes, I just realized from my end that it is not working. Sorry for rushing
> to the conclusion.
>
> Could you try to remove the line "H1 H2" from this part: "LOOP \n H1 H2"
> in the ZAFF.prep file?
>
> I am not sure why ZAFF did that to make the water a triangle. But
> hopefully, this is the reason for the water hydrogens being over
> coordinated.
>
> Best regards,
> Zhen.
>
> _____________________
>
> Zhen Li <http://lizhen62017.wixsite.com/home>, Ph.D.,
>
> He/Him/His,
>
> The Merz Research Group <http://merzgroup.org>,
>
> Rm. 287, Department of Chemistry,
>
> 578 S Shaw Ln., Michigan State
> <https://www.google.com/maps/search/578+S+Shaw+Ln.,+Michigan+State?entry=gmail&source=g>
> University,
>
> 48824, MI.
> ------------------------------
> *From:* DIPANKAR DAS 20012 <dipankard20.iiserbpr.ac.in>
> *Sent:* Friday, March 28, 2025 11:03 PM
> *To:* Li, Zhen <lizhen6.chemistry.msu.edu>
> *Cc:* amber.ambermd.org <amber.ambermd.org>
> *Subject:* Re: [AMBER] Help with ZINC Paramterisation using MCPB.py
>
> Hi, thanks for the reply.
> I actually tried following what you mentioned relating to ZAFF, however, I
> still ended up getting the same Warning/ Note, post the tLEaP process.
>
> Kindly find attached the image. Additionally, find attached the leap input
> and log file.
>
> Thanks and regards,
> Dipankar
>
>
> On Sat, Mar 29, 2025 at 8:14 AM Li, Zhen <lizhen6.chemistry.msu.edu>
> wrote:
>
> Hi Dipanka,
>
> For the MCPB.py problem. Are you able to visualize the fchk file using
> GaussView or Avogadro? It seems to be an issue with the generation of fchk
> file in the formchk step, not an error from MCPB.py.
>
> For the ZAFF issue, you probably need to add a TER between ZN and O in the
> 3ks3.amber.pdb to tell tLEaP that they are two residues, not one.
>
> Hope it helps.
>
> Best regards,
> Zhen.
>
>
>
> _____________________
>
> Zhen Li
> <https://urldefense.com/v3/__http://lizhen62017.wixsite.com/home__;!!HXCxUKc!0r6AHR2nUW_N0ggdZqapVptkOLVCioMsCfzLRjiyn0AseTYEqECo3Wf3DA5R5KUqmouTWHV_Ns5O42NMHO8Bas-1xGllpsZHmQ$>,
> Ph.D.,
>
> The Merz Research Group
> <https://urldefense.com/v3/__http://merzgroup.org__;!!HXCxUKc!0r6AHR2nUW_N0ggdZqapVptkOLVCioMsCfzLRjiyn0AseTYEqECo3Wf3DA5R5KUqmouTWHV_Ns5O42NMHO8Bas-1xGm9VFZb4A$>
> ------------------------------
> *From:* DIPANKAR DAS 20012 via AMBER <amber.ambermd.org>
> *Sent:* Tuesday, March 25, 2025 10:37 AM
> *To:* amber.ambermd.org <amber.ambermd.org>
> *Subject:* [AMBER] Help with ZINC Paramterisation using MCPB.py
>
> Dear Amber Community, following the tutorial for MCPB.py
> <
> https://urldefense.com/v3/__https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php__;!!HXCxUKc!wKUxp5h_CZp9fSeyVnvShxYa3x9bQC3-CxmkFs-hoifU-PnYIJ75PKPlfAQ_dPpftSgYeSeWACxE6wXOc3KPKDs$
> >. I tried to
> parametrise the Zinc ion using MCPB following the same naming convention
> used in the tutorial.
>
> I was able to run Gaussian and perform the Merz-Kollman RESP charge
> calculation for the large model. My system of interest is human carbonic
> anhydrase II (PDB ID: 3d92). However, post the gaussian calculation, I got
> the following error when I try to run this command :
>
> MCPB.py -i 3d92.in
> <https://urldefense.com/v3/__http://3d92.in__;!!HXCxUKc!0r6AHR2nUW_N0ggdZqapVptkOLVCioMsCfzLRjiyn0AseTYEqECo3Wf3DA5R5KUqmouTWHV_Ns5O42NMHO8Bas-1xGkFkEwZDg$>
> -s 2
>
>
> The error :
> "*===================Generate the Initial frcmod file=============*
> * *
> ******************************************************************
> Atoms which has changed the atom types: [1417, 1454, 1797, 4058, 4059]
> 91-HID.1417-NE2 : NB --> Y1
> 93-HID.1454-NE2 : NB --> Y2
> 116-HIE.1797-ND1 : NB --> Y3
> 258-ZN.4058-ZN : ZN --> M1
> 259-MOH.4059-O : oh --> Y4
> ==================Using the Seminario method to solve the problem.
> Traceback (most recent call last):
> File "/home/cclab/miniconda3/envs/AmberTools23/bin/MCPB.py", line 670, in
> <module>
> gene_by_QM_fitting_sem(smpdbf, ionids, xstru, stfpf, prefcdf, finfcdf,
> File
>
> "/home/cclab/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py",
> line 729, in gene_by_QM_fitting_sem
> crds = get_crds_from_fchk(chkfname, len(atids))
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File
>
> "/home/cclab/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/pymsmt/mol/gauio.py",
> line 369, in get_crds_from_fchk
> for line in fp:
> File "<frozen codecs>", line 322, in decode
> UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0:
> invalid start byte"
>
> Could someone help me figure out where I am going wrong. Kindly find the
> attached zipped folder.
>
> Additionally, I have tried to use ZAFF for the parameterization of Zinc.
> Following the ZAFF tutorial for parameterizing, however, I encountered an
> issue during the production run using pmemd, where the simulation
> terminated with the following error:
>
> > "Hydrogen atom 4101 appears to have multiple bonds to atoms 4102 and
> 4101, which is illegal for SHAKEH.
> > Exiting due to the presence of inconsistent SHAKEH hydrogen clusters."
>
> I believe this issue might be related to the warnings/notes I received
> after the tleap process:
>
> > "1-4: angle 4101 4102 duplicates bond ('triangular' bond) or angle
> ('square' bond)
> > 1-4: angle 4101 4103 duplicates bond ('triangular' bond) or angle
> ('square' bond)
> > 1-4: angle 4102 4103 duplicates bond ('triangular' bond) or angle
> ('square' bond)"
>
> I suspect that my water molecule may not be properly coordinating with the
> Zinc ion, which could be contributing to this issue. I would appreciate any
> insights on whether this could be a possible cause and how to ensure
> correct coordination.
>
> To provide more context, kindly find attached the following files, the
> tleap input file, the log file and the input PDB used in the study.
>
> I would appreciate any insights or suggestions on how to resolve this
> issue. Thank you for your time and guidance.
> MCPB.py.zip
> <
> https://urldefense.com/v3/__https://drive.google.com/file/d/1GKOSz2pk7Baq2Ph31ZLAgozHEZJEKg0c/view?usp=drive_web__;!!HXCxUKc!wKUxp5h_CZp9fSeyVnvShxYa3x9bQC3-CxmkFs-hoifU-PnYIJ75PKPlfAQ_dPpftSgYeSeWACxE6wXOkgEWgCc$
> >
>
>
>
> Thanks and regards
> Dipankar
>
>
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