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where can I find the file of toppar_prot_na_all.str?
#19918 01/22/09 02:11 PM
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Hi,
I want to do the simulation for the phosphorylated threonine. Would you please tell me where I can find the file of toppar_prot_na_all.str? As I can't find the file in my local server.
Thanks a lot!

Re: where can I find the file of toppar_prot_na_all.str?
dawn1313 #19919 01/22/09 05:20 PM
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Check the 'toppar/stream' subdir of CHARMM distributions for all of the *.str files.

Re: where can I find the file of toppar_prot_na_all.str?
rmv #19920 01/25/09 03:54 PM
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Hi,

Thank you very much for your quick response.
I have another two problems as follows.
Thanks a lot!

1. There are two atoms 'OT' and 'HT' in the phosphorylated residue that have no coordinates. How to solve it?

2. When I do the minimization,should the beginning of the file be as follows, which means the 'stream' command is still necessary
( I think later the following commands are unnecessary:
PATCH THP1 prot 164
AUTOGEN ANGLE DIHE), is it right?

-------------------

OPEN UNIT 1 CARD READ NAME top_all27_prot_na.rtf
READ RTF CARD UNIT 1
CLOSE UNIT 1

OPEN UNIT 1 CARD READ NAME par_all27_prot_na.prm
READ PARA CARD UNIT 1
CLOSE UNIT 1

stream toppar_prot_na_all.str

Re: where can I find the file of toppar_prot_na_all.str?
dawn1313 #19921 01/25/09 05:36 PM
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PDB coord files often have some name variations (residues, atoms) compared to the CHARMM topology files; perhaps there's an atom in your coord that should be renamed to OT. If not, it should be possible to use IC (Internal Coordinate; intcor.doc) commands to place the OT atom. Use HBUILD to place missing H atoms.

If you have saved the resulting PSF, it is not necessary to re-apply the PATCH and AUOTGEN; that information has been incorporated into the PSF.

Re: where can I find the file of toppar_prot_na_all.str?
rmv #19922 01/26/09 01:03 PM
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It works after I change the atom name of O3p to OT and O to OT1.
I really appreciate your help!


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