I came across with this error while trying to create a psf file. I retyped the changed file name in the txt file and it still gave the same error. Could you please help me?
''too many arguments specified MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.''
Are you using VMD? After which statement you write do you see this error? This is the "typical" error message given by VMD during psf generation, so there may be many different reasons. You should be more specific..
Yes, VMD. Actually, I was practising (not to use auto psf gen) following the namd tutorial, which suggests to practise with ubiquitin. Here the txt file:
package require psfgen
topology top all27 prot lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment U {pdb ubqp.pdb}
coordpdb ubqp.pdb U
guesscoord
writepdb ubq.pdb
writepsf ubq.psf
and then I typed in Tk Console the following:
% source ubq.pgn
You should change the file name to all27_prot_lipid.inp, as I did, but the same error came up again.
Instead of writing all the commands in a script file (here, I guess the script has been saved as ubq.pgn) once, and then use source command from TK console (which is fine, if you're sure that your script will run), write each statement in the TK console one by one and press enter in between. Determine the statement after which the error comes up. My guess is that pdbalias statements will not problematic. Probably, guesscoord causes the error, but I cannot be sure unless you inform me the exact erroneous statement.
Ayse, the error is in the second line: topology top all27 prot lipid.inp
The actual file contains underlines, like this: topology top_all27_prot_lipid.inp
You said you changed the file name, but forgot the top_
Worked for me!
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