Dear Shveta, I have seen similar trends with PRODRG. I recommend you to use other molecular modeling programs like Hyperchem or Maestro to get more consistent geometric parameters for small molecules. Once you know the bondlengths and bond angles from aforesaid molecular modeling programs, you can use sketcher (CCP4) to define them manually. Save it to the monomer library and you are all set to run them in Refmac .
or You can use Phenix.elbow or phenix.reel to load the coordinates of the small moleucle and optimize with AM1 (semi-empirical), then you should get reasonable geometirc parameters suc as bond length, bond angles and etc. Hope this helps ! Cheers, Krishna Krishna Chinthalapudi, PhD Hannover Medical School On Mon, Jan 9, 2012 at 7:13 AM, Shveta Bisht <shv...@mbu.iisc.ernet.in>wrote: > Dear all > > I have generated a refmac cif file for a molecule using PRODRG. I used > JME editor to draw the molecule and ran PRODRG online with the > options: Chirality-Yes, Charges-Reduced and EM-Yes. Please check the > attachments for the molecule drawing and the expected bond lengths as > listed in the PRODRG generated cif file. There are some unusual > values. I have listed them below along with the likely explanations > (just guesses). > > DRG CAR CAK single 1.390 0.025 > DRG CAQ CAB single 1.390 0.025 > DRG CAT CAI single 1.390 0.020 > All three are C-C single bonds where one of the carbons belong to > aromatic ring. This might lead to a short bond, although 1.39 seems to > be too short for this. > > DRG CAI NAL double 1.340 0.022 > DRG CAP NAL single 1.340 0.022 > Here N and both the carbons are sp2 hybridization, so there can be > delocalization of electrons. Thus both bonds (single and double) are > of similar length. > > DRG CAP CAA double 1.530 0.025 > As mentioned above, if pi (unhybridized) electrons of CAP are involved > in CAP NAL bonding, then CAP CAA double bond essentially becomes a > single bond with 1.53 bond length. > > I need advise on the way I have run prodrg and the explanations for the > results. > Is it common to observe such values? Or it is due to the alternating > single and > double bonds in this structure. > > -- > Shveta Bisht > Ph.D. Student, > Prof. M R N Murthy's Group, > Molecular Biophysics Unit, > Indian Institute of Science > Bangalore-12 > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > >
