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biotin parameters
#22637 10/28/09 01:02 PM
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FranciT Offline OP
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Hi everybody,
I'm trying to build a biotinilated peptide, i found some biotin parameterization but when I tried to build the peptide i found some problems and i think that my problems are related to the parameters. Do you have some advices about it?
thank you in advance

Attached Files
biotOut.txt (6.85 KB, 428 downloads)
biotb4.txt (1014 Bytes, 396 downloads)
Re: biotin parameters
FranciT #22638 10/28/09 01:28 PM
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You have randomly changed the order of commands
IC PARA
IC SEED
IC BUIL
HBUILD
What you have will not work.

You want to use CHARMM formatted coordinate files rather than PDB as far as possible (PDB is an export/import format).
The PSF does not change when you minimize, so no need to save it all the time.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22643 10/28/09 02:49 PM
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thank you very much for your help,
but when I tried to build this structure, this is the error related to parameters, how can I do?
thank you in advance

<CODES>: No bond parameters for 26 ( CN1 ON1 )
<CODES>: No torsion parameters for 47 ( CP1 NN2U CN1 ON1 )
<CODES>: No torsion parameters for 48 ( CP1 NN2U CN1 NN2U)
<CODES>: No torsion parameters for 53 ( CP1 NN2U CN1 ON1 )
<CODES>: No torsion parameters for 54 ( CP1 NN2U CN1 NN2U)
<CODES>: No torsion parameters for 62 ( ON1 CN1 NN2U HN2 )
<CODES>: No torsion parameters for 63 ( ON1 CN1 NN2U HN2 )
<CODES>: No torsion parameters for 69 ( NN2U CN1 NN2U HN2 )
<CODES>: No torsion parameters for 73 ( NN2U CN1 NN2U HN2 )
<CODES>: A TOTAL OF 9 MISSING PARAMETERS

Re: biotin parameters
FranciT #22657 10/28/09 09:20 PM
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It seems that the RTF and PARAmeter files you have are incomplete wrt biotin (or possibly not used in the correct way); you could check with the person/group that provided the files.
Or you add the missing parameters to the parameter file - this could be straightforward if parameters for similar groups are already available.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22688 11/02/09 11:42 AM
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FranciT Offline OP
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thank you for your help. Unfortunately i don't understand what happens to my input file because it doesn't work. Can you help me?

i attached all the file in use input/output
and the params.
thank you very much in advance

Attached Files
b3.txt (684 Bytes, 354 downloads)
b3Out.txt (7.64 KB, 609 downloads)
parBna.txt (241.16 KB, 414 downloads)
topBna.txt (108.04 KB, 520 downloads)
Re: biotin parameters
FranciT #22689 11/02/09 12:36 PM
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Remove the BOMLEV -2 command.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22690 11/02/09 02:42 PM
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FranciT Offline OP
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in this way I had the error

BTN GLY GLY GLY THR

***** LEVEL 0 WARNING FROM <CHARMM> *****
***** Unrecognized command: BTN
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

but in the top and param file I added the BTN group, so I don't know why it doesn't recognize BTN.
thank you in advance

Re: biotin parameters
FranciT #22691 11/02/09 05:04 PM
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Because BTN is not a CHARMM command, which is exactly what the error message tells you.

I think you need something like this:
read sequence card
* peptide part
*
4
GLY GLY GLY THR
gene pept setup ! possibly with FIRST/LAST specifications

read sequence btn 1
gene btn setup

In addition you will need to create the bond between biotin and the peptide, possiblby using a PATCh command which requires the appropriate PRES to be present in your RTF.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22694 11/03/09 09:40 AM
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thank you so much i'll try to build the peptide using your precious advices.
Thank you again

Re: biotin parameters
lennart #22695 11/03/09 11:18 AM
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FranciT Offline OP
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Here I am again,
sorry if I look like too intrusive,
so I follow your advice Prof. Lennart, and I generated a pdb, unfortunately the coordinates for the btn residue still non defined and i don't understand why
to link the two segments i modified PRES LINk (as it possible to see down here. (i used this patch because the link that the biotin form with the residue is similar to a peptidic link, i've just changed the name of the atoms)
thank you again




PRES LINK 0.00 ! linkage for IMAGES or for joining segments
! 1 refers to previous (N terminal)
! 2 refers to next (C terminal)
! use in a patch statement
! follow with AUTOgenerate ANGLes DIHEdrals command
BOND 1C1 2N
IMPR 2N 1C1 2CA 2HN 1C1 1C10 2N 1O1
IC 1O1 1C10 1C1 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1C10 *1C1 1O1 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C10 1C1 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C1 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C1 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000

Attached Files
b3inp.txt (661 Bytes, 383 downloads)
b3Out.txt (8.97 KB, 369 downloads)
b3.pdb (5.32 KB, 292 downloads)
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