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normal backward.py error

  • arnis
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9 years 10 months ago #3897 by arnis
backward.py error was created by arnis
Hi all,

I've encountered the following error using backward.py.
Checking dependencies:
backward.py ... /home/arnis/Desktop/REVERSE/backward.py
grompp ... /usr/bin/grompp
mdrun ... /usr/bin/mdrun
Traceback (most recent call last):
  File "/home/arnis/Desktop/REVERSE/backward.py", line 644, in <module>
    struc = Structure(options["-f"].value,strict=options["-strict"].value)
  File "/home/arnis/Desktop/REVERSE/backward.py", line 410, in __init__
    d12.append(d12[-1])
IndexError: list index out of range

This occurs on both Ubuntu 11.04/14.04 with python 2.7.x. I used the martini2.2P FF with the protein topology modified to have all asp/glu residues in their neutral state (ASP0/GLU0). The command I issued was:
./initram.sh -f MD.pdb -p charmm.top -to charmm36 -keep

Any suggestions on how to fix this?

Thanks in advance,

Arnis

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9 years 10 months ago #3899 by arnis
Replied by arnis on topic backward.py error
Problem solved - I took a look at backward.py and realized that protonated ASP/GLU aren't in the default list of residues. I added mapping definitions for the residues according to the backward.py tutorial and everything worked out nicely.

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5 years 8 months ago #7767 by anjukris
Replied by anjukris on topic backward.py error
Could you tell me how you did this? I am new to this.

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5 years 6 months ago #7811 by riccardo
Replied by riccardo on topic backward.py error
Hi,

Sorry for the late reply. That's how you can create a mapping file for a protonated state starting from a neutral form (or, actually, that's how you create a mapping file for a molecule which has *1 more atom* than an arbitrary molecule for which you have a mapping file).
Assuming you download backward for GMX 5 or >, incl. mapping files for the amino acids. You'll find, in the "Mapping" folder, the file "asp.amber.map". Looks like this:

[ molecule ]
ASP

[ martini ]
BB SC1

[ mapping ]
amber

[ atoms ]
1 N BB
2 HN BB
3 CA BB
4 HA BB
5 CB SC1 BB BB
6 HB1 SC1 BB BB
7 HB2 SC1 BB BB
8 CG SC1 SC1 BB
9 OD1 SC1
10 OD2 SC1
11 HD2 SC1
12 C BB
13 O BB

[ ... ]


If you want to add a proton, then you need to add one line and (potentially) renumber the lines, getting:

[....]

[ atoms ]
1 N BB
2 HN1 BB
3 HN2 BB
 4 CA BB
5 HA BB
6 CB SC1 BB BB
7 HB1 SC1 BB BB
8 HB2 SC1 BB BB
9 CG SC1 SC1 BB
10 OD1 SC1
11 OD2 SC1
12 HD2 SC1
13 C BB
14 O BB

[ ... ]

Note that I have done it almost randomly. This has to match your atomistic topology. Actually, you should modify the mapping file *according* to your protonated atomistic topology for, say, ASP.

Hope this helps

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