Dear Aashish,
Thank you so much. You are right. By mistake, whilst working very hard to get a very troublesome ion-ligand calculation working with GAMESS-US, I copied the optimised coordinates of the small_opt into the large_mk file.
Again, thank you.
Anthony
Kind regards
Dr Anthony Nash PhD MRSC
Senior Research Scientist
Nuffield Department of Clinical Neurosciences
RMCR Kellogg College
University of Oxford
http://www.kellogg.ox.ac.uk/
________________________________
From: Aashish Bhatt <aashish.ph16221.inst.ac.in>
Sent: 16 August 2021 12:25
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] resp2.chg file is missing whilst processing 3rd stage of MCPB.py
Dear Anthony
Kindly check your large file. I suspect that you have calculated resp
charge for the small file instead of the large file.
I have faced the same issue but when I supplied the correct file it worked
for me.
Kindly look into the following link
http://archive.ambermd.org/201801/0249.html
Best Regards
Aashish
On Mon, Aug 16, 2021 at 4:49 PM Anthony Nash <anthony.nash.ndcn.ox.ac.uk>
wrote:
> Dear all,
>
> This is related to my earlier email "MCPB.py - ComplexWarning...", which I
> moved past onto the 3rd stage of MCPB.py, the assigning of RESP charges.
>
> For clarity, everything has worked up until I tried working on the 6th
> metal site in my protein.
>
> I am seeing the following error:
>
> ******************************************************************
> * *
> *======================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...
> MMP1_ca_1104_large_mk.esp
> CAUTION: THE VDW RADIUS OF ATOMIC NUMBER 20IS UNKNOWN AND HAS
> BEEN SET TO1.80 ANGSTROMS IN THE GAMESS CALCULATION.
>
> Unit 3 Error on OPEN: resp1.chg
> OR HERE...
> Traceback (most recent call last):
> File "/home/ubuntu/miniconda3/envs/AmberTools21/bin/MCPB.py", line 692,
> in <module>
> resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids, ff_choice,
> File
> "/home/ubuntu/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/pymsmt/mcpb/resp_fitting.py",
> line 472, in resp_fitting
> chgs = read_resp_file('resp2.chg')
> File
> "/home/ubuntu/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/pymsmt/mcpb/resp_fitting.py",
> line 18, in read_resp_file
> fp = open(fname, 'r')
> FileNotFoundError: [Errno 2] No such file or directory: 'resp2.chg'
>
>
> Digging around, the code in resp_fitting.py executes:
>
> resp -O -i resp1.in -o respl1.out -p resp1.pch -t resp1.chg -e
> MMP1_ca_1104_mk_large.esp -s resp1_calc.esp
>
> This does not produce the resp1.chg file, so further calculations cause
> the script to crash.
>
> This is my input:
> original_pdb corrected_ca_1104.pdb
> group_name MMP1_ca_1104
> cut_off 2.8
> ion_ids 5808
> ion_mol2files calcium_atom_1104.mol2
> large_opt 1
> force_field ff99SB
> software_version gms
>
>
> I'm now pushing hard against a fast-approaching manuscript resubmission.
> Any suggestions are massively appreciated.
>
> Thanks
> Anthony
>
>
> Kind regards
> Dr Anthony Nash PhD MRSC
>
> Senior Research Scientist
> Nuffield Department of Clinical Neurosciences
> RMCR Kellogg College
> University of Oxford
> http://www.kellogg.ox.ac.uk/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 16 2021 - 05:00:02 PDT
