Most likely, there is some error in topology. Please post your topology/parameter/link files for the unconventional residue....
2149
Nic
nsteussy
Mar 5, 2012 10:14 am
Yes. I have had this happen when I had to create a novel amino acid (oxidized cysteine) and didn't set it up to 'link' with the normal amino acids....
2150
Krisztina Feher
feher_krisztina
Mar 5, 2012 10:57 am
Hi Nic, thanks a lot! This was the solution as you suggested: I forgot to add the new residue into the link file to be patched with PEPT. SInce the involved...
2151
Weidong Hu
lakesu
Mar 5, 2012 7:16 pm
Dear All, Â I would like to use CNS 1.2 to calculate peptide structure based on NMR restraints. I am wondering where can I get a water refinement script...
2152
Alexey Denisov
denisrita
Mar 6, 2012 7:51 pm
I am running CNS 1.2 calculations of NMR structure of symmetric DNA duplex (like (CGAAATTTCG)2 ) and would like to use NCS restraints included in the...
2153
Alexey Denisov
denisrita
Mar 8, 2012 8:49 pm
I solved this puzzle with help of the XPLOR manual. The absent NCS file "ncs_restrain.dat" for symmetry in NMR structure calculations should be like: flags ...
2154
mscsu
Mar 26, 2012 6:23 pm
Hi Everyone, I was wondering if the cns libraries have definitions for 2-mercaptoethanol and 2-hydroxyethyl disulfide. If not, how can I generate those...
2155
Ed Pozharski
pozharski
Mar 26, 2012 6:30 pm
Use Hic-Up database, e.g http://xray.bmc.uu.se/hicup/BME/index.html Otherwise, xplo2d is a standalone program (part of USF) and prodrg is a server you can use....
2156
Mike Osborne
ozzy672003
Mar 26, 2012 8:33 pm
Hi Everyone I was wondering if anyone has a working topology and param file (CNS) for one of the following ligands with protons to allow me to do a structure...
2157
Paul Adams
PDAdams@...
Apr 3, 2012 9:01 pm
Dear Colleagues, on behalf of the selection committee I'd like to draw your attention to the the Trueblood award: ...
2158
Sanishvili, Ruslan
rsanishvili@...
Apr 3, 2012 10:15 pm
Dear Colleagues, We would like to point out that the application deadline for the 5th annual CCP4 Summer School "From data collection to structure refinement...
2159
f570518
Apr 4, 2012 4:29 pm
Dear All, I installed cns-solve.1.21 coupled with Aria2. When I tried to run aria2 I got the error message as: EntityValueError: USER ERROR...
2160
Ed Pozharski
pozharski
Apr 4, 2012 4:37 pm
Since the error is raised by Aria23/src/py/aria/cns.py, this is not a CNS-question. Try asking your question in Aria discussion board. ... -- After much deep...
2161
jruhym
Apr 5, 2012 8:53 pm
Hi, I have a situation in which I would like to have different scale factors for NOE and hydrogen bond restraints using annealing. I looked on the "input...
2162
Gerard DVD Kleywegt
gerard@...
Apr 11, 2012 2:15 pm
Are you an aspiring science communicator who has a wonderful way with words? The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is looking for an ...
2163
Sanishvili, Ruslan
rsanishvili@...
Apr 12, 2012 3:09 pm
Dear Colleagues, This is friendly but final reminder that Tuesday, April 17 is the application deadline for the fifth annual CCP4 Summer School "From data...
2164
sunil
sktewarybt1993
Apr 14, 2012 1:25 pm
Hi I am facing the problem of putting correct label in the MTZ file. Ctruncate (ccp4 GUI) programme uses some default label which is not sufficient to run...
2165
mscsu
Apr 25, 2012 3:07 am
Hi Everyone, I am having some trouble with make_cv.inp. I am using cns 1.3. My issue is that I have a hkl file that I want to convert to a cv file. My hkl file...
2166
Ed Pozharski
pozharski
Apr 25, 2012 12:31 pm
... I assume that your "hkl" file is in CNS format. "cv" file is not any different, make_cv.inp simply adds an extra column to define the test set. Other...
2167
Jeanne Cambefort
cambefort@...
May 16, 2012 5:15 pm
Hello, I'm new on CNS. I would like to generate N structures during a molecular dynamics. I employed model_anneal.inp downloaded on...
2168
Ed Pozharski
pozharski
May 16, 2012 6:33 pm
... if you didn't touch traj_freq, it should... post the log-file, there might be a clue there. -- Oh, suddenly throwing a giraffe into a volcano to make water...
2169
Ed Pozharski
pozharski
May 17, 2012 8:32 pm
... model_anneal_3HOS_X.pdb where X=1-10. Check your output folder. This is a concern though %CNSsolve> error encountered: File model_anneal_3HOS_1_traj.crd...
2170
Jeanne Cambefort
jeannecambefort
May 17, 2012 9:11 pm
Hello, I'm sorry I reply late. I think I can exploit my results by calculating the FRET Efficiency this way: ...
2171
Jeanne Cambefort
jeannecambefort
May 18, 2012 2:15 am
... Well all the snapshots seem to be created at the same time, and they seem to be very similar. But they are created. I did not see this error. ... Of course...
2172
Ed Pozharski
pozharski
May 18, 2012 2:54 am
... That's OK - snapshots are indeed created at the end of each trial, all at the same time. As for the snapshots being very similar - they are only separated...
2173
pingyangliu
May 23, 2012 8:46 pm
Hi I try to create a generate file from a protein pdb file, but the program stopped because the residue LLP not found in topology files. Now I have the...
2174
Ed Pozharski
pozharski
May 23, 2012 9:38 pm
You don't need to add anything to protein.top etc. Just add your .top and .param files for the ligand to the list at the top of generate.inp ... -- "Hurry up...
2175
gcpvanzundert
May 30, 2012 4:36 pm
Hi, I was wandering how the Fourier transform function is defined in CNS. When 'ft' is used, is it a normal fast-fourier-transform call or is there more to it?...
2176
Axel Brunger
brunger@...
May 30, 2012 4:41 pm
Please read my paper in Acta Cryst A which describes the method implemented in both X-PLOR and CNS. A. T. Brunger, A memory-efficient fast Fourier...
2177
Gerard DVD Kleywegt
gerard@...
May 31, 2012 4:52 pm
Hi all, E3 ubiquitin ligase is responsible for flagging proteins for degradation by transferring ubiquitin from a donor protein onto the molecule to be...
