[AMBER] error regarding MCPB.py

From: Hemant Kisan <hemantkisna12.gmail.com>
Date: Wed, 11 Sep 2019 18:59:16 +0300

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
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)
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
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
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.
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.

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 - 09:00:02 PDT
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