Re: AW: AW: problem with pdb psf files!

From: Jacqueline Schmidt (
Date: Tue Sep 04 2012 - 06:06:06 CDT

Dear Norman, Can I add my psb/psf files (for the surface+water) to the peptide psf/files created by psfgen using the psfgen? If I can do this, it will solve my problem. Thanks Jackie ________________________________ From: Norman Geist <> To: 'Jacqueline Schmidt' <> Cc: Namd Mailing List <> Sent: Tuesday, September 4, 2012 2:59 AM Subject: AW: AW: namd-l: problem with pdb psf files! Hi,   what is seriously not the problem, is the initial structure as the psf doesn’t care about coordinates.   So are you sure that your psf contains this improper parameters?   I still don’t understand why you don’t use your program to build up only the initial structure with your molecules as pdb, and just throw it through psfgen. Why do you need to create the psf yourself?   As you seem to be familiar with codes, you could check the namd code that produces the error, maybe add some debug lines of output, and check what namd is reading from your psf. Could you send us a diff output of a psfgen generated psf and your own one?   Norman Geist. [] Im Auftrag von Jacqueline Schmidt Gesendet: Montag, 3. September 2012 18:01 An: Norman Geist Cc: namd Betreff: Re: AW: namd-l: problem with pdb psf files!     Dear Norman, Thanks for your reply. Some of these systems are peptides on the clay surfaces that are bound through periodic box in xy directions. I had to create the pdb psf files for the surfaces through my own code and  then added  another section to put the peptide on it. The question I asked below is for a peptide in solution (as a stating point). Vmd loads my pdb psf file with no flaw. All connectivities are correct. However namd gives me an error looking for an improper coefficient. What is so wired is that the CT1 C O NH1 is always in anypeptide and I really wonder why I get this error while the psfgen generated files wouldn't cause this error. Could this be because my structure is for from the equilibrium? or it is due to the formatting and I have to rearrange my code to change the writing sequences as in psfgen? thanks again Jackie ________________________________ From:Norman Geist <> To: 'Jacqueline Schmidt' <> Cc: Namd Mailing List <> Sent: Monday, September 3, 2012 3:18 AM Subject: AW: namd-l: problem with pdb psf files! Hi,   also as a 1st friendly comment, what exactly is the problem when using psfgen?   Are you able to load the pdb/psf pair in vmd? Maybe vmd will tell you something.   Usually md tools must somehow identifiy parts of a structure by some fixed properties. I remember that I got some serious problems when I wrote a program that had to connect molecules of to pdbs at specific binding sites by automatic adjusting and fitting. The problems was about amino acids, that had another order than the default is. This caused that I could not identify N or C-terminals very comfortable to set the right TER lines there.   And as I know, NAMD also threats some things about hydrogens hard coded. So maybe you also change something that makes it impossible for namd to interpret the files correctly. But the developers can maybe tell you more.   You could check the code of namd, to see what maybe happens, or just stay with the order namd seems to expect.   Norman Geist. [] Im Auftrag von Jacqueline Schmidt Gesendet: Montag, 3. September 2012 04:45 An: namd Betreff: namd-l: problem with pdb psf files!   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 except two things 1) the order of the atoms 2) It does not include the right 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 jackie

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