The problem here is that the names you're giving to the segids (A and B) need to be in quotes.
If you change your script to read vector do (segid = "A") (resid 1:17) vector do (segid = "B") (resid 18:34) you should be all right. --JK On May 30, 2008, at 9:30 AM, Silke Johannsen, Anorganisch-Chemisches Inst. wrote: > Hello Charles > > I tried now to use the dna_refi script but I get always this error: > > X-PLOR>vector do (segid = A) (resid 1:17) > Assuming literal string "A" > SELRPN: 525 atoms have been selected out of 1053 > X-PLOR>vector do (segid = B) (resid 18:34) > SELRPN: 525 atoms have been selected out of 1053 > %VECTOR-ERR: Variable type mismatch between both sides of equation.: > vector do (segid = B) (resid 18:34) > ^ > %VECTOR-SCPARS-ERR: Assignment aborted.: > vector do (segid = B) (resid 18:34) > > and after a while the program seems to calculate and stops with > this error > message > > InternalDynamics::step: large timestep detected. Halving. > > The thing is also that I do not have just the normal bases but also > three > modified ones in a row which coordinate metal ions. Where I have to be > careful and change things? You also mentioned that I should use a > completely > symmetric potential, but I am beginner and do not know how to do or > check > this. Furthermore I do not have RDCs, do you thing it is possible > to get a > proper structure without them? > > thanks a lot > > silke > > > On Tue, 15 Apr 2008 16:59:07 -0400 > Charles at Schwieters.org wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Silke-- > > I want to calculate a DNA duplex structure with a palindromic > sequence from NMR data, means I have the NOE restraints only from > half of > the duplex. In my case the center is not a normal Watson-Crick base > pair but > two modified bases, which coordinate linear a metal ion. At first I > just > duplicated the NOE restraints for the others, but the structures > looked > really bad. So the idea was to calculate the upper half, copy it > for the > lower one and set it in the right way together. Is there any > possibility to > do so with xplor NIH? And can I optimize the whole structure > afterwards? > > > You should really use a completely symmetric potential if when > you > include all atoms- all terms should have the proper symmetry. In > addition you should use the NCS potential as in the eginput/ > dna_refi > example scripts. > > I hope this helps-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+ > <http://mailcrypt.sourceforge.net/> > > iD8DBQFIBRcWPK2zrJwS/lYRAg7VAJ9nXwhUnF6EW3Pwyn66ccL2x0IXlQCfUCJS > babHNj13noehXtS2RE29r0k= > =6nNp > -----END PGP SIGNATURE----- > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
