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Amber-MD / cpptraj

Biomolecular simulation trajectory/data analysis.
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problem regarding "change" command in cpptraj #994

Closed saikat0003 closed 3 months ago

saikat0003 commented 2 years ago

Dear all,

I have converted my topology file with added PDB information (like chain ID and renumbering PDB) using "parmed". However, the previously mentioned information still missing in output file (like rmsf). I have gone through the following link: http://archive.ambermd.org/201709/0275.html http://archive.ambermd.org/202106/0042.html

Here is my steps:

parm rgs01-1.rgs01.parm7 addPDB rgs01.pdb parmout rgs01-1-mod.rgs01.parm7 go

change oresnums of :1-317 min 32 max 348 change chainid of :1-317 to A change oresnums of :318-449 min 60 max 191 change chainid of :318-449 to D out remap.dat

It shows the error: .................................................................................. Changing chain ID of residue TYR:441 from 'D' to 'D' Changing chain ID of residue LEU:442 from 'D' to 'D' Changing chain ID of residue ASN:443 from 'D' to 'D' Changing chain ID of residue LEU:444 from 'D' to 'D' Changing chain ID of residue LEU:445 from 'D' to 'D' Changing chain ID of residue ASN:446 from 'D' to 'D' Changing chain ID of residue ASP:447 from 'D' to 'D' Changing chain ID of residue LEU:448 from 'D' to 'D' Changing chain ID of residue GLN:449 from 'D' to 'D' [out remap.dat] Warning: Data set 'outremap.dat' not found. Error: Data set with name 'outremap.dat' not found. 'out remap.dat': Invalid command or expression. 1 errors encountered reading input. TIME: Total execution time: 0.0169 seconds. Error: Error(s) occurred during execution.

I want to put information like residue number and chain id in the topology file.

Thanks and Regards,

Saikat Pal

drroe commented 2 years ago

The error arises because 'out' is not a recognized command. What did you intend with 'out remap.dat'? By itself, 'out' is not a command, though it is a keyword for many other commands.

drroe commented 2 years ago

Perhaps what you wanted instead of out was parmwrite out <file> to write a topology?

drroe commented 1 year ago

Did parmwrite out work for you?

drroe commented 3 months ago

Since there hasn't been any movement on this in a while I'm going to close it. Feel free to reopen if it is still an issue.