Kindly check your Fe.mol2 file
I think you have wrong something
460-FE1.7429-FE : f --> M1
It look like fluorine not iron.
Best Regards
Aashish
On Wed, Sep 11, 2019 at 11:32 PM Hemant Kisan <hemantkisna12.gmail.com>
wrote:
> Dear Amber users
> I need a help with regards to following query
> I am unable to get final .frcmod file on execution of MCPB.py -i
> 1jpz_b_H-renum.in -s 2. Although I am getting pre.frcmod file which is
> 1jpz_mcpbpy_pre.frcmod.
> Additionally on terminal following error message has been displayed
> 400-CP1.6416-SG : s --> Y1
> 459-HEM.7361-NA : nd --> Y2
> 459-HEM.7372-NB : nd --> Y3
> 459-HEM.7380-NC : nd --> Y4
> 459-HEM.7388-ND : nd --> Y5
> 460-FE1.7429-FE : f --> M1
> Traceback (most recent call last):
> File "/home/kddubey/softwares/amber16/bin/MCPB.py", line 657, in <module>
> ff_choice, gaff, frcmodfs, watermodel)
> File
>
> "/home/kddubey/softwares/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_pre_frcmod_file.py",
> line 516, in gene_pre_frcmod_file
> raise pymsmtError("Could not find VDW parameters/radius for "
> NameError: global name 'pymsmtError' is not defined.
>
> As per the suggestion of following link
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
> I started working on a metalloprotein pdb file 1jpz.pdb. This
> metalloprotein contain resname HEM consisting of Fe3+ and porphyrin unit
> (2-). This pdb file is also having with substrate with resname 140.
> The steps that I have followed are narrated below:
>
> 1) I have removed one of the chain which is chain a then saved the chain b
> 1jpz_b.pdb.
> 2) As per the suggestion I have saved HEM residue to a different pdb file
> as HEM.pdb which is devoid of FE 3+. Similarly I have save FE coordinate as
> FE1.pdb separately.
> 3) Subsequently I have saved cysteine 400 to different pdb file as CP1.pdb.
> 4) On the other hand I have saved residue resname 140 to a separate pdb
> file called NPG.pdb and replaced all resname 140 by NPG.
> 5) Now by using reduced command I have generated subsequent files having
> with hydrogens and saved the above separate pdb files to HEM_H.pdb,
> CP1_H.pdb, NPG-H.pdb. While adding I make sure that all charges are
> maintained as HEM with 4- and CP1 should devoid with H at sulphur and NPG
> with 1- charge. Also I have executed pdb4amber to generate new pdb files.
> 6) By using antechamber I have generated corresponding .mol2 files and
> generated HEM.mol2, CP1.mol2, FE1.mol2, NPG.mol2 files
> 7) Subsequently using parmchk2 I have generated HEM.frcmod , CP1.frcmod ,
> NPG.frcmod files.
>
> 8) Using webserver H++ I have generated .top and .crd files and
> subsequently I have generated corresponding pdb file as well which further
> followed by pdb4amber.
> 9) Now I have combined all pdb file and made only one pdb file to which
> further I subjected to pdb4amber.
> 10) Now using MCPB.py -i 1jpz_b_H-renum.in -s 1 command I have generated
> small, standard and large as well as fc.com files.
> 11) After successfully computed gaussian09 calculation I have generated
> fchk file from small model and RESP charge from larger model.
> 12) NOW IS THE PROBLEM
> When I am executing following command MCPB.py -i 1jpz_b_H-renum.in -s 2
> I am able go get pre.frcmod file but not final.frcmod file.
>
> Kindly help me in figure out what went wrong.
>
> Thanks
> Hemanta
> --
> Hemanta K. Kisan, Ph.D.
> Post-Doctoral Research Fellow
> Prof. Sason Shaik's Group
> Institute of Chemistry
> The Hebrew University of Jerusalem, Givat Ram Campus,
> Jerusalem-91904, Israel
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Received on Wed Sep 11 2019 - 22:00:02 PDT
