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Re: Calculation of rmsd from NAMD coor file judkil21 09/24/22 06:40 PM
The pdb files are necessarily read with an option (RESID or SEGI or CHAIN) because they are not native files. And if I don't add one of these options, charmm will write me that I am missing atoms.
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Molecular Dynamics Jump to new posts
Re: Calculation of rmsd from NAMD coor file judkil21 09/24/22 06:18 PM
For bomlev -5 : In miscom, paragraph 14,

"-5,-4 Limit exceeded type of errors" this is the only line where I don't see what exceeded type of errors means.

As I'm in the learning phase, it would be a value of -1 that I should put.

In test/c39test/readpdb.inp we call directly the necessary segment when we read the pdb file, interesting
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Molecular Dynamics Jump to new posts
Re: Calculation of rmsd from NAMD coor file lennart 09/24/22 02:16 PM
READ COOR PDB takes several options that make it possible to avoid splitting the file: RESI to override residue numbers and instead use RESID and SEGID information. CHAIN <chain id> or SEGI <segi> reads just the lines in the file that contain the specified CHAIN/SEGI information (which may or may not be the same as the PSF SEGI since it is just a filter applied to the reading of the PDB coordinate file). There are also options to use or skip certain lines (HETATOM, ATOM, specified residue names) or to map residue names in the file to names in PSF.

see test/c39test/readpdb.inp for examples. io.info may not be quite up-to-date on these options.
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Molecular Dynamics Jump to new posts
Re: Calculation of rmsd from NAMD coor file rmv 09/23/22 08:13 PM
One thing to know is that CHARMM is not very graceful about reading PDB files; it is regarded as an import/export format only, and not a native file type. The Script Archive forum has a number of posts on the topic. Files with multiple segments usually require splitting into one file per segment.
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