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
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Re: [AMBER] cpptraj: modification of topologies/trajectories from Daniel...
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Re: [AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap from Daniel Roe on 2021-06-07 (Amber Archive Jun 2021)
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Re: [AMBER] How to fix the numbering of amino acid that got shifted in t...
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Here is following my steps:
parm rgs01-1.rgs01.parm7addPDB rgs01.pdbparmout rgs01-1-mod.rgs01.parm7go
change oresnums of :1-317 min 32 max 348change chainid of :1-317 to Achange oresnums of :318-449 min 60 max 191change chainid of :318-449 to Dout 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
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Received on Wed Oct 12 2022 - 17:00:02 PDT
