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zlyhhl Offline OP
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hello, everyone
i am a new user for charmm. There are much difference between the PDB format from RCSB and charmm format. but how do I convert PDB format into charmm format?
thanks very much!

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CHARMM does read the standard PDB format - could you be more specific about the differences you have observed?
Note that for reading the sequence you can only have one segment (eg pepdtide chain or nucleic acid strand) in the PDB file. The PDB format is best treated as an import/export format, and CHARMM's own format is recommended for normal use.
See examples in the Script Archive.


Lennart Nilsson
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Originally Posted By: lennart
CHARMM does read the standard PDB format - could you be more specific about the differences you have observed?
Note that for reading the sequence you can only have one segment (eg pepdtide chain or nucleic acid strand) in the PDB file. The PDB format is best treated as an import/export format, and CHARMM's own format is recommended for normal use.
See examples in the Script Archive.


Could you please tell me what should I do to convert pdb file that contains more than one segment?

Last edited by fiona; 09/19/13 07:25 PM.
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rmv Online Content
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Rick Venable
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Recent CHARMM versions allow you to specify the chain id to the READ command, eg:
READ SEQUENCE PDB CHAIN B NAME 1xyz.pdb

This may be helpful in some, but not all cases.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  lennart, rmv 

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