Dear Eugene, I think I know what the problem is. When generating a single psf file from two strands of DNA (like the dickerson dodecamer duplex), you should either specify each strand with a different segment id. (e.g. strand A and strand B). By default, if you don't specify a segment id, the molecule is considered as a monomer, so residue 1 is connected to 2, 2 to 3, and so on. (So also cross-strand 12 is connected to 13)
or you should check your PSF file, and remove any connectivities that connect the two strands. For the dickerson (dimer of 12 nucleotides), remove any connections (bonds, angles, dihedrals) between residues 12 and 13. Regards, Ramon On 02/11/2010 06:00 PM, [email protected] wrote: > Send Xplor-nih mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xplor-nih digest..." > > > Today's Topics: > > 1. snow leopard (Sanaz Dovell) > 2. Re: snow leopard ([email protected]) > 3. Re: snow leopard ([email protected]) > 4. Problems with eginput DNA structure calculations > (DeRose, Eugene (NIH/NIEHS) [C]) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 10 Feb 2010 13:43:33 -0500 > From: Sanaz Dovell<[email protected]> > Subject: [Xplor-nih] snow leopard > To: [email protected] > Message-ID:<[email protected]> > Content-Type: text/plain; charset=us-ascii > > I recently upgraded my mac to Snow Leopard and now XPLOR-NIH does not work. > Any suggestions? > > Thanks. > > > ------------------------------ > > Message: 2 > Date: Wed, 10 Feb 2010 14:13:31 -0500 > From: [email protected] > Subject: Re: [Xplor-nih] snow leopard > To: Sanaz Dovell<[email protected]> > Cc: [email protected] > Message-ID:<[email protected]> > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Sanaz-- > > >> I recently upgraded my mac to Snow Leopard and now XPLOR-NIH does not work. A >> ny suggestions? >> >> > > I worked through this issue on the mailing list in the last couple of > weeks. I believe the solution is to remove > bin.Darwin_8_x86/libgcc_s.1.dylib. > > Please let me know if this does it. > > best regards-- > Charles > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+<http://mailcrypt.sourceforge.net/> > > iEYEARECAAYFAktzBVsACgkQPK2zrJwS/lYWLwCfU2uBgTOXAQNLPkL1KXKogc1h > idoAn1jGvTU2pGY83Ria3SJKNImH/QcQ > =0VAm > -----END PGP SIGNATURE----- > > > ------------------------------ > > Message: 3 > Date: Wed, 10 Feb 2010 16:35:33 -0500 > From: [email protected] > Subject: Re: [Xplor-nih] snow leopard > To: Sanaz Dovell<[email protected]> > Cc: [email protected], [email protected] > Message-ID:<[email protected]> > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > > Hello Sanaz-- > > >> Do you mean to remove the physical file from the bin.Darwin_8_x86 = >> folder? If so, I did remove it, but I still get the message >> >> xplor not configured for platform: Darwin_10_x86 >> >> > sorry, the other part is to do this: > > echo "Darwin_8_x86 Darwin_9_x86 Darwin_10_x86">> arch/equivList > > Charles > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+<http://mailcrypt.sourceforge.net/> > > iEYEARECAAYFAktzJqUACgkQPK2zrJwS/lartACfezAZAr7V60L7Qxo1t5tUYD4R > HcQAniyjtXQMlD5muJQFO2oy7u7eBSQB > =HC+r > -----END PGP SIGNATURE----- > > > ------------------------------ > > Message: 4 > Date: Thu, 11 Feb 2010 10:57:04 -0500 > From: "DeRose, Eugene (NIH/NIEHS) [C]"<[email protected]> > Subject: [Xplor-nih] Problems with eginput DNA structure calculations > To: "[email protected]"<[email protected]> > Message-ID:<c7999300.6a27%[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > I am trying to use the dna_refi.inp script to compute the structure of the > Dickerson dodecamer with some ribose sugar substitutions. Unfortunately the > structures, especially the base geometries are significantly distorted. > > I have noticed that the sample refine_full.inp script generates a good > structure for the sample DNA calculation in eginput/dna_refi as long as the > psf file provided, dna_new.psf, is used, i.e., > > REMARK FILENAME="test_full_nocoup_1.sa" > REMARK =============================================================== > REMARK > overall,bonds,angles,improper,vdw,noe,cdih,dipo,rama,ncs,orie,plan,coup,dcsa > REMARK energies: 7430.46, 56.3133, 593.507, 10.1168, 76.1481, 114.733, 0, > 8004.42, -1340.35, 306.109, -946.373, 17.2073,106.849, > > However, if a new structure file is generated using eginput/dna/dna.inp the > geometric energy terms increase dramatically and the base geometry is > significantly distorted, i.e., > > REMARK FILENAME="test_full_nocoup_1.sa" > REMARK =============================================================== > REMARK > overall,bonds,angles,improper,vdw,noe,cdih,dipo,rama,ncs,orie,plan,coup,dcsa > REMARK energies: 37050.2, 2329.45, 9680.19, 15715.1, 915.524, 822.767, > 0.241548, 7967.06, -1315.5, 1283.43, -777.791, 4.82553, > > The use of this psf file in the sample eginput/dna/full_ring_03.inp > calculation also results in high energies: > > REMARK FILENAME="full_ring_03_1.sa" > REMARK =============================================================== > REMARK overall,bonds,angles,improper,vdw,noe,cdih,xdip,rama,ncs,orie,plan > REMARK energies: 31243, 2993.69, 9027.05, 18832.2, 398.815, 653.736, > 5.06793, 1587.24, -3273.41, 1713.71, -704.531, 9.39292 > > Upon comparison of the dna_new.psf file provided and the newly created psf > file, I noticed that the new file has more improper terms defined. > > As a side note, the sample refine_full.py calculation also produces high > energies with a significant number of experimental violations: > > REMARK ------------------------------------------------------------ > REMARK summary Name Energy RMS Violations > REMARK summary total 77782.66 785 > REMARK summary ANGL 934.87 2.039 295 > REMARK summary BOND 252.82 0.018 23 > REMARK summary CDIH 21.94 1.652 2 > REMARK summary IMPR 76386.18 28.835 46 > REMARK summary NCS 651.75 > REMARK summary ORIE -854.54 > REMARK summary PLAN 7.04 > REMARK summary RAMA -1267.03 > REMARK summary VDW 57.52 2 > REMARK summary csa 43.94 2.235 44 > REMARK summary jcoup 5.63 0.160 22 > REMARK summary noe 53.87 0.053 0 > REMARK summary rdcs 1488.67 0.537 351 > > Any suggestions on what might be causing the problem with the psf files will > be greatly appreciated. > > Thanks, > Eugene > > Eugene DeRose, Ph.D. > NIEHS NMR Laboratory Manager > Global Health Sector > SRA International, Inc. > Contractor to NIEHS/DIR > National Institute of Environmental Health Sciences > Research Triangle Park, NC 27709 > 919.541.1981 voice > 919.541.5707 fax > [email protected] > www.niehs.nih.gov > www.sra.com > Enhancing Human Health Around the World Everyday > _______________________________________________ Xplor-nih mailing list [email protected] http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
