MALIGN3D Top files which worked well using Modeler 4 are giving me this
error :
fndatmi_284E> Beginning atom index for a residue out of bounds: 0
0
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
I am using the following script
# MALIGN3D
READ_ALIGNMENT FILE = 'pair.aa'
SET ATOM_FILES = '1.pdb' '2.pdb'
SET FIT_ATOMS = 'CA'
MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off
If anybody has seen this problem, please help.
Thank you
…
[View More]Michael Buck
************************************************
Michael Buck
NCSU Genetics
mjbuck(a)unity.ncsu.edu
Phone (919)515-5759
Fax (919)515-3355
http://www4.ncsu.edu/~mjbuck
*************************************************
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Dear users,
I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have.
When I tell Modeller to execute the "check_alignment" command, I get the following message:
rdpir___E> alignment sequence not found in PDB file: 1
./pXXXX.pdb
#######################################################################################################################################
The alignment I have is:
>P1;pXXXX
structureX:…
[View More]pXXXX:.::.:::::
CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM*
>P1;pAveM
structure:pAveM:2::211:::::
-----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV*
>P1;Ali2
sequence:Ali2::::::::
VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV*
#######################################################################################################################################
Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb)
Can somebody help me?
Thank you very much,
Paola
--
dott. Paola D'Alessio (PhD student)
Universita' degli Studi di Salerno
Dipartimento Scienze Farmaceutiche
via Ponte Don Melillo, 84084 Fisciano (Sa), Italy
tel.+39 089 962822; e-mail: pdalessio(a)unisa.it
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Hi,
I got selenomethionines on a template structure and the program does not
find
selenium in topology library. Have you got selenium parametrized
(radii...) or
any suggestions in my next moves?
thanks a lot.
fab
