From: Jacqueline Schmidt (jacqueline_schmidt_1983_at_yahoo.com)
Date: Sun Sep 02 2012 - 21:36:17 CDT
Dear Namd users,
I have got a problem with my pdb/psf file running with NAMD. I have done some coding to transfer the car/mdf (insight format) to the pdb/psf file ( just a friendly first comment: please don't refer me to psfgen because I have a surface in my system which can not be dealt with top file)
When I load the files into the vmd everything seems to be perfect. However when I run the files in NAMD I get the error that : CAN'T FIND IMPROPER PARAMETERS FOR CT1 C O NH1
the error message is self explanatory; however, I don't understand why I am getting this error at all, because the indicated atom types are the backbone atoms which every FF parameters should be already in the parm file.
The only difference between my pdb psf files is that I write the non-hydrogen atoms in any residue first followed by the list of hydrogen names/ff-types. Is this a problem??
As a test I made the pdb/psf files with psfgen too. Everything between the files is again the same expect two things 1) the order of the atoms 2) It does not include the write c-terminal atoms with their FF-type indicated in the top file. I simply treats the last carbon as C C (name and FF-type) instead of C CC and only one oxygen at the end which is O O instead of OT1 OC, and the OT2 is not in the file at all (it was in my original pdb that feeded into the psfgen though).
I hope someone can help me please, I am really confused
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