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martinize.py
- rguixa
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11 years 7 months ago #1136
by rguixa
martinize.py was created by rguixa
Hi there,
I am trying to build a topology file that includes the correct parameters for a ElNeDyn network by using the martinize script. I downloaded the last version but got this error when using the -elnedyn option:
Traceback (most recent call last):
File "./martinize.py", line 4374, in <module>
options = option_parser(args,options,lists,version)
File "./martinize.py", line 368, in option_parser
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
KeyError: '-elnedyn'
Upon inspecting the script, I decided to uncomment line 272 which is actually commented out:
("-elnedyn", Option(bool, 0, False, "Use Elnedyn mapping and parameters with elastic network")),
After doing so, I don't get any error message, however, I don't see any information on the ElNeDyn in the .itp file (regardless of the -ef and -eu values I use along).
Just in case I am not using a proper pdb file, I used as a sample the pdb file included in the ElNeDyn tutorial (1A8G.pdb) to run the martinize script. Again, no errors and no EleNeDyn parameters on the .itp files generated. No matter what -ef and -eu values I use, I always get the same topology files.
This is the standard line I am running:
./martinize.py -f 1A8G.pdb -o 1A8G_CG.top -x 1A8G_CG.pdb -ss 1A8G.dssp -p backbone -cys auto -v -name 1A8G -p All -nt -elnedyn -ef 500 -eu 0.9
Is there anything I am doing wrong?
Thanks in advance,
Ramon
I am trying to build a topology file that includes the correct parameters for a ElNeDyn network by using the martinize script. I downloaded the last version but got this error when using the -elnedyn option:
Traceback (most recent call last):
File "./martinize.py", line 4374, in <module>
options = option_parser(args,options,lists,version)
File "./martinize.py", line 368, in option_parser
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
KeyError: '-elnedyn'
Upon inspecting the script, I decided to uncomment line 272 which is actually commented out:
("-elnedyn", Option(bool, 0, False, "Use Elnedyn mapping and parameters with elastic network")),
After doing so, I don't get any error message, however, I don't see any information on the ElNeDyn in the .itp file (regardless of the -ef and -eu values I use along).
Just in case I am not using a proper pdb file, I used as a sample the pdb file included in the ElNeDyn tutorial (1A8G.pdb) to run the martinize script. Again, no errors and no EleNeDyn parameters on the .itp files generated. No matter what -ef and -eu values I use, I always get the same topology files.
This is the standard line I am running:
./martinize.py -f 1A8G.pdb -o 1A8G_CG.top -x 1A8G_CG.pdb -ss 1A8G.dssp -p backbone -cys auto -v -name 1A8G -p All -nt -elnedyn -ef 500 -eu 0.9
Is there anything I am doing wrong?
Thanks in advance,
Ramon
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- xavier
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11 years 7 months ago #1139
by xavier
Replied by xavier on topic martinize.py
Hey,
This might be confusing. The philosophy of martinize for ElNeDyn has changed a bit. Now the ELNeDyn approach has been switched to a "force field". The -elnedyn option does not exist anymore
So you should not uncomment the line of course but use the flag -ff elnedyn and -ff elnedyn22 to include the latest refinement of the MARTINI side chains; -elnedyn22P if water and sidechains are used with dipoles.
This might be confusing. The philosophy of martinize for ElNeDyn has changed a bit. Now the ELNeDyn approach has been switched to a "force field". The -elnedyn option does not exist anymore
So you should not uncomment the line of course but use the flag -ff elnedyn and -ff elnedyn22 to include the latest refinement of the MARTINI side chains; -elnedyn22P if water and sidechains are used with dipoles.
rguixa wrote: Hi there,
I am trying to build a topology file that includes the correct parameters for a ElNeDyn network by using the martinize script. I downloaded the last version but got this error when using the -elnedyn option:
Traceback (most recent call last):
File "./martinize.py", line 4374, in <module>
options = option_parser(args,options,lists,version)
File "./martinize.py", line 368, in option_parser
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
KeyError: '-elnedyn'
Upon inspecting the script, I decided to uncomment line 272 which is actually commented out:
("-elnedyn", Option(bool, 0, False, "Use Elnedyn mapping and parameters with elastic network")),
After doing so, I don't get any error message, however, I don't see any information on the ElNeDyn in the .itp file (regardless of the -ef and -eu values I use along).
Just in case I am not using a proper pdb file, I used as a sample the pdb file included in the ElNeDyn tutorial (1A8G.pdb) to run the martinize script. Again, no errors and no EleNeDyn parameters on the .itp files generated. No matter what -ef and -eu values I use, I always get the same topology files.
This is the standard line I am running:
./martinize.py -f 1A8G.pdb -o 1A8G_CG.top -x 1A8G_CG.pdb -ss 1A8G.dssp -p backbone -cys auto -v -name 1A8G -p All -nt -elnedyn -ef 500 -eu 0.9
Is there anything I am doing wrong?
Thanks in advance,
Ramon
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