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Prepare non-heme irons, 2Fe(III)-2S input files
#38037 08/14/20 03:24 AM
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Hello all,I'm working with a protein having a non-heme diiron 2FE-2S center.I need to distinguish the two irons to represent the data separately.
So I added iron 1 and iron 2 parameters in the MASS of the .rtf file.
But when running the charmm program to output psf and crd files, the following error is reported in the log file:
WARNING FROM DECODF - COULD NOT CONVERT STRING
FE1
ZERO WILL BE RETURNED.
WARNING FROM DECODF - COULD NOT CONVERT STRING
FE2
ZERO WILL BE RETURNED.
PARRDR> NOTE: atom type "FE1 " is removed from previous group
PARRDR> NOTE: atom type "FE2 " is removed from previous group

PARRDR> ALL ANGLES HAVE POSITIVE MINIMA
Is my way of dealing with the 2 iron 2 sulfur system wrong, or is it a problem of preparation parameters?
Thank you very much for your reply, I added the main part of the input rtf file and the log file to the attachment magager.
PS:I have tried three solutions,None resolved:
1.Use dos2unix command to convert to linux file
2.Use tr -d'\n' new-file.rtf command line,new-file, rtf file is emptied;
3.Using the same FE-O atom type will show duplicate parameters.

Attached Files
2FE-2S.zip (2.92 KB, 10 downloads)
SHA1: 715b3f2be384a992f3b953f126a458cc199c9e7a
Re: Prepare non-heme irons, 2Fe(III)-2S input files
dengwenhao #38038 08/14/20 02:45 PM
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The error message indicates a text string was found where a number was expected; check your syntax carefully.


Rick Venable
computational chemist

Re: Prepare non-heme irons, 2Fe(III)-2S input files
dengwenhao #38039 08/15/20 04:17 PM
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Thank you very much, Professor, I solved the above problem !
I encountered a new problem when adding residue.
No matter how I modify the PDB file of the custom residue TOL, the following error always appears(PS:rtf and prm files run smoothly):
CHARMM> read sequence pdb append unit 10
**** Warning **** The following extraneous characters
were found while command processing in CHARMM
APPEND
MAINIO> Sequence information being read from unit 10.
TITLE> *

RESIDUE SEQUENCE -- 1 RESIDUES
TOL

CHARMM> generate TOL first none last none warn setup

***** ERROR in GENIC ***** Residue 'TOL ' was not found.
I would like to ask how I should solve this problem. The TOL file has been checked many times.
Best wishes!

Re: Prepare non-heme irons, 2Fe(III)-2S input files
dengwenhao #38040 08/15/20 04:41 PM
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The error indicates that the TOL residue is not defined in any of the topology files that were read, and does not necessarily mean there is a problem with the PDB file.

Note that the READ SEQUence command does not have an APPEND option, which accounts for the warning message.


Rick Venable
computational chemist

Re: Prepare non-heme irons, 2Fe(III)-2S input files
dengwenhao #38042 08/16/20 05:06 PM
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Thank you, professor, I successfully passed the RTF and PRM files, and produced the set-up PDB file.
My substrate toluene PDB file and water molecules cannot produce hydrogen atom coordinates.I still have problems after many attempts to modify
I guarantee that the toluene PDB file and the water PDB syntax format are consistent with the polypeptide chain.
The following is the output setup part of the substrate and water coordinates:
ATOM 13034 HB1 TOL 1 9999.0009999.0009999.000 1.00 0.00 TOL
ATOM 13035 HB2 TOL 1 9999.0009999.0009999.000 1.00 0.00 TOL
ATOM 13036 HB3 TOL 1 9999.0009999.0009999.000 1.00 0.00 TOL
ATOM 13037 CF4 TOL 1 75.927 88.019 46.254 1.00 80.16 TOL
ATOM 13038 CF3 TOL 1 75.538 88.850 45.198 1.00 78.28 TOL
ATOM 13039 HD1 TOL 1 9999.0009999.0009999.000 1.00 0.00 TOL
ATOM 13040 CF2 TOL 1 75.995 90.168 45.103 1.00 75.34 TOL
ATOM 13041 HE1 TOL 1 9999.0009999.0009999.000 1.00 0.00 TOL
ATOM 13042 CF1 TOL 1 76.866 90.672 46.070 1.00 77.38 TOL
ATOM 13043 HZ TOL 1 9999.0009999.0009999.000 1.00 0.00 TOL
ATOM 13044 CF5 TOL 1 76.802 88.540 47.219 1.00 80.62 TOL
ATOM 13045 HD2 TOL 1 9999.0009999.0009999.000 1.00 0.00 TOL
ATOM 13046 CF6 TOL 1 77.273 89.851 47.126 1.00 79.46 TOL
ATOM 13047 HE2 TOL 1 9999.0009999.0009999.000 1.00 0.00 TOL
ATOM 13048 OH2 TIP3 1 71.271 90.653 44.758 1.00 40.88 CRYW
ATOM 13049 H1 TIP3 1 9999.0009999.0009999.000 1.00 0.00 CRYW
ATOM 13050 H2 TIP3 1 9999.0009999.0009999.000 1.00 0.00 CRYW
ATOM 13051 OH2 TIP3 2 72.799 83.466 47.750 1.00 37.38 CRYW
ATOM 13052 H1 TIP3 2 9999.0009999.0009999.000 1.00 0.00 CRYW
ATOM 13053 H2 TIP3 2 9999.0009999.0009999.000 1.00 0.00 CRYW
ATOM 13054 OH2 TIP3 3 71.240 103.153 33.026 1.00 36.51 CRYW
ATOM 13055 H1 TIP3 3 9999.0009999.0009999.000 1.00 0.00 CRYW
ATOM 13056 H2 TIP3 3 9999.0009999.0009999.000 1.00 0.00 CRYW
Attach the two parts of the command in my inp file:
open read unit 10 card name tolu.pdb
read sequence pdb resi unit 10
generate TOL first none last none warn setup
rewind unit 10
read coor pdb unit 10 append
close unit 10

open read unit 10 card name cryw.pdb
read sequence pdb resi unit 10
generate CRYW noangle nodihedral setup
rewind unit 10
read coor pdb unit 10 append
close unit 10

ic fill preserve
ic parameters
ic build
hbuild sele all end

join TOL renum
join CRYW renum

I have read page 47 of the book <>>. (From above book:The elements of the newly created arrays for the Cartesian coordinates are first set to 9999.00000).
I really don’t know where I went wrong. Thanks again to the professor and good health!

Re: Prepare non-heme irons, 2Fe(III)-2S input files
dengwenhao #38043 08/16/20 05:27 PM
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PS:bomblevel -1
wrnlevel 5
prnlev 10

Re: Prepare non-heme irons, 2Fe(III)-2S input files
dengwenhao #38044 08/16/20 06:43 PM
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A detailed analysis of the output log file is usually required as part of solving problems such as these; you should examine the CHARMM response to each command for hints about where the problem might be.


Rick Venable
computational chemist


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