Hi Everyone, I am trying to run a SA job. ... %NEXTF-ERR: EOF or ERROR encountered on input: ^ %NEXTF-ERR: EOF or ERROR encountered on input: ^ %PARSER error...
677
Joe Krahn
joekrahn
May 29, 2003 4:07 am
Raji, It is hard to determine your problem without seeing a few more lines of the output. Is your PDB file missing an END statement? The PDB END statement is...
678
raji
raji77
May 29, 2003 7:08 am
Hi, Thanks to all of you for writing back. No, my pdb file is not missing an 'END' statement; nor are there any brackets etc. missing or incomplete. I have...
679
Daan van Aalten
vdava@...
May 29, 2003 7:09 am
Hi Raji Have you tried making a toplogy for your ligand with the PRODRG server at http://davapc1.bioch.dundee.ac.uk/prodrg ? try starting from a drawing with...
680
Kay Diederichs
kay.diederichs@...
May 29, 2003 7:43 am
Raji, is that a CNS executable compiled with the ifc compiler under Linux? If so, I have seen similar problems like you. This can be fixed by a patch to the...
681
purvis_alan
May 29, 2003 12:33 pm
I was hoping that someone could shed some light on how it attach a small ligand covalently to a side chain. This is a relatively simple process for sugar...
682
Zeljko Dzakula
zdz@...
May 29, 2003 3:23 pm
Hi Raji, it seems that you did not get my previous email, so here it goes again: your NCS matrix #4 is incorrectly defined, with two opening parentheses...
683
raji
raji77
May 29, 2003 3:30 pm
Yes, I've had similar issues recently. But, this time I am running the job on a Dec-Alpha. The problem, I'm embarassed to say, was that I had double opening...
684
Zeljko Dzakula
zdz@...
May 29, 2003 3:40 pm
Hi, try the patch statement. If for any reason you don't want to use a patch, you can use NOE restraints to keep the bonded atoms close. You can even use NOEs...
685
Leonard Thomas
thomasle@...
Jun 6, 2003 9:36 pm
Hi All, After running the composite omit map routine in CNS, I went to view the maps in O and keep getting the following error in O cannot fill the desired...
686
Zeljko Dzakula
zdz@...
Jun 6, 2003 9:50 pm
Hi, if you look at the script composite_omit_map.inp, you will see the following code: xray write map if ( &map_format = "ezd" ) then type=ezd else type=cnx ...
687
dujt01
Jun 9, 2003 8:47 pm
Dear everyone, I have learnt CNS for calculation of peptide and want to plan my experiment! Now I am not sure that CNS can be used for phosphopeptide structure...
688
Zeljko Dzakula
zdz@...
Jun 9, 2003 9:08 pm
Hi, you can certainly use CNS for any kind of molecules, including phosphopeptides, but it may require a little work to properly set up the topology and the ...
689
matthew hogg
Matthew.Hogg@...
Jun 9, 2003 9:36 pm
Hi all, When trying to calculate a combined phase map using the model_map.inp script I get the following error: %XDOEVAL-ERR: reciprocal space object MAP_FOM...
690
matthew hogg
Matthew.Hogg@...
Jun 10, 2003 2:03 am
I got several replies to my problem only to discover that I can't type I typed "combine", not "combined";, as the map type. The error I got, though, did not...
691
Thomas Barends
t.barends@...
Jun 10, 2003 12:25 pm
Hello CNS-users, I'm trying to refine a twinned crystal structure in CNS by simulated annealing. I've set the Wa weight (geometry/X-ray terms) to -1, so that ...
692
BASU
dhaksbala
Jun 10, 2003 12:56 pm
Dear cns-users, I am solving a structure which has space group R3 and i have refined the structure but the freer value is not lowered. The R-value is 28% and...
693
Poul Nissen
nissen@...
Jun 10, 2003 1:08 pm
Besides the usual things on refinement etc., two suggestions: 1) check for twinning 2) check for lower symmetry - perhaps monoclinic with 3-fold NCS Poul -- ...
694
K.A.Kulkarni
mahan_2001
Jun 10, 2003 5:12 pm
Hi, Before giving any suggestions let me ask u some questions. 1)How much is the data completion and what is the quality of data (R merge)? 2)Have u used NCS...
695
lgurunathan
Jun 10, 2003 8:58 pm
Hello, I am having a problem in connecting the carbohydrate moeity NAG(N- acetyl glucosamine) with the Asn residue of my protein.I used the following script in...
696
motop pes
motoppes6
Jun 10, 2003 10:44 pm
Hi all, I have a problem with D amino acids in CNS. I generated the mtf file from sequence and applied the patch LTOD to invert some natural aminoacids....
697
K.A.Kulkarni
mahan_2001
Jun 11, 2003 8:14 am
Hi, U need to check 3 things. Have u defined B1N in ur topology files ? Define the segids properly in patch definitions. "carbo_i_segid_1="A";...
698
Vijay Reddy
reddyv@...
Jun 12, 2003 5:18 pm
Dear all, To put it out as information (news/views) for the community interested in crystal screening using robotics: Syrrx, a structural genomics company,...
699
Jason
jkyano
Jun 14, 2003 12:28 pm
Hi All, I am having a problem renaming ILE CD1 in windows 2000. When I modify the generate.inp script like so: {* some atoms may need to be renamed in the...
700
tirsia_net
Jun 16, 2003 12:16 pm
Hi all, does anyone know how to substiture a residue in CNS? I would like to change any residue to a cysteine with a spin label for which I already have the...
701
matthieu
matthieu_nmr
Jun 16, 2003 2:25 pm
hello ! i would like to fix my [2Fe-2S] cluster during anneal_cv.inp calculations using cns_solve 1.1 and cannot find how to do it ? Could anyone help me on...
702
matthew hogg
Matthew.Hogg@...
Jun 18, 2003 6:23 pm
Hi all, I'm trying to use generate_easy.inp with a selenomethionine derivative in CNS. No matter how I alter the pdb file to tell cns I have an MSE residue I...
703
matthew hogg
Matthew.Hogg@...
Jun 18, 2003 7:16 pm
Please ignore previous post. Seems I only figure out my problem AFTER I post a question to the bulletin board!...
704
Tara Sprules
tarasprules
Jun 20, 2003 4:34 pm
Hi, I was trying to add ha proton chemical shift restraints to my structure calculation and found that they were not improving things very much- in fact the...
705
Andrew Wong
whyandrew
Jun 21, 2003 12:33 pm
Hi First sorry for being off-topic, but I thought this would be a good place to ask as most other ppl won't have much experience in this. We thinking of...
