FW: psf generation for a small non-peptide molecule - again

From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Mon Sep 29 2008 - 17:21:16 CDT

Hello Sorry for bothering you with such trivial questions, but I would really appreciate some ideas regarding these issues. The PDB that I am working with was exported from crystallographic CIF file, and atom type allocation was done by hand. Especially I am not sure for the proper type of the oxygen in carbonyl groups (I used type no. 70 'O') and nitrogene in tertiary amine groups (I have used type 'NR1'). I have also corected the file in Molefacture as atom type 'OS' from the PDB was converted to element 'OS' and exported an XBGF file which I used further for AutoPSF, but still 10 atoms apear us unknowns (unparametrized) Please find attached the PDB and the selection of the atoms with problems. Can you please give me some ideas about what could be wrong with those atom types allocations ? Also while runing Autopsf I got the message "I couldn't find the original pdb to assign connectivity. Using autogenerated connectivity only" although I had both the XBGF and the PDB file loaded in VMD.
 
Many thanks > From: vchindea_at_hotmail.com> To: namd-l_at_ks.uiuc.edu> Subject: psf generation for a small non-peptide molecule> Date: Fri, 26 Sep 2008 00:18:40 +0300> > > Hello everybody> > As I am new to the NAMD program I have run into problems with psf generation. > > As top_all27_prot_lipid topology file supplied with NAMD tutorials is specificaly made for proteins and lipids I am not sure I am using correct atom types for my molecule. > Chemically-wise this molecules contains Sp3 carbons, polar and nonpolar hydrogens, hydroxyl, ester and ether oxygens, tertiary amine nitrogens. Particullary I am not sure what are the proper atom types for ether oxygen and tertiary amine nitrogen in this topology file. Do you have any suggestions ?> > Further more is there any other, more general maybe, topology file that should be more suitable for this kind of modelling tasks ?> > Many thanks and kind regards> > Vlad Chindea> _________________________________________________________________> Connect to the next generation of MSN Messenger > http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline
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