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Setup, I/O, and Basic questions
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Check for other messages, esp. from opening the input trajectory files. If the files were not produced by CHARMM or have been modified by some other program, the file headers may not conform to what is expected by CHARMM, which can cause problems
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Setup, I/O, and Basic questions
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Add the following two commands to your input-- PREF SHOW These will produce listings that indicate what features were added at compile time, including any parallel keywords.
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Setup, I/O, and Basic questions
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Just to be very specific: For the coor hbond command you shouldnot have to worry about donors and acceptors - coor hbond knows about this from the RTF. Did you actually try the command I provided? Please do, it is quite illustrative. It is often
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Setup, I/O, and Basic questions
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Then use four separate lines. If you have very many different values you can put them in a text file (one per line), which you can read into CHARMM variables using the get command (see miscom.doc)
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CHARMM-GUI
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Hello, I am using CHARMM GUI generated files to run the simulation with Amber. I noticed that the minimization file doesnt contain the command to run it with periodic boundary conditions. May I ask what is the reason for that? Thank you!
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