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Where to get the top and par files for retinal?
#20427 03/15/09 09:54 PM
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Hi Charmmers:

In the latest release of Charmmm force field, I only found parameters for fret. Do you know where to get the top and par files for retinal? Thanks!

Re: Where to get the top and par files for retinal?
Hailiang #20428 03/15/09 10:01 PM
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Check the toppar_all22_prot_retinol.str file in the 'stream' subdir ...

Re: Where to get the top and par files for retinal?
rmv #20429 03/16/09 01:48 AM
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Thanks rmv. But I still just find Fenretinide, not retinal or retinol.

Re: Where to get the top and par files for retinal?
Hailiang #20430 03/16/09 07:26 PM
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When I looked in the distributed file, I found both retinal (RESI RTAL) and retinol (RESI RTOL); here's the full list of residues in that file--

RESI BTE2 0.00 ! 2-Butene, adm jr.
RESI HEP3 0.00 ! 1,3,5-heptatriene
RESI 13DB 0.00 ! 1,3-dibutene
RESI 13DP 0.00 ! 1,3-dipentene
RESI DMB1 0.00 ! 2-methyl-1,3-butadiene
RESI DMP1 0.00 ! 4-methyl-1,3-pentadiene
RESI DMP2 0.00 ! 2-methyl-1,3-pentadiene
RESI CROT 0.00 ! 2-buteneamide,N,3-dimethyl (crotonamide)
RESI PACP 0.00 ! p-acetamide-phenol
RESI MECH 0.00 ! 1,6,6-trimethyl-2-ethene-cyclhexene
RESI TMCH 0.00 ! 1,2,6,6-tetramethylcyclohexene
RESI FRET 0.00 ! fennretinide, nomenclature consistent with retinol
RESI RTOL 0.00 ! retinol, nomenclature from PDB
RESI RTAL 0.00 ! retinal, nomenclature from PDB based on retinol
RESI RTAC -1.00 ! all-trans-retinoic acid, nomenclature from PDB
RESI PRAC -1.00 ! 2-propenoic acid
RESI PROL 0.00 ! 3-propenol (1-hydroxy-2-propene)
RESI PRAL 0.00 ! 1-propenal
RESI SCH1 0.00 ! Schiff's base model compound 1, deprotonated
RESI SCH2 1.00 ! Schiff's base model compound 2, protonated
RESI SCH3 1.00 ! Schiff's base model compound 3, protonated

Re: Where to get the top and par files for retinal?
rmv #20431 03/17/09 04:03 PM
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Thank you so much rmv. I should have look it up more carefully.

By the way, I need to simulate the structure of a "modified" retinal which is covalently bound with a Lysine-N after dehydration. Since this structure is quite common, I am just wondering whether there is already some corresponding top and par file. By the way, if I have to modify and top and par files myself, is there some handbook or tutorial which instructs modifying CHarmm par files? Thanks again for any kindly help!

Re: Where to get the top and par files for retinal?
Hailiang #20432 03/17/09 05:12 PM
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Once again, I must suggest that you look through toppar_all22_prot_retinol.str very, very carefully.

Re: Where to get the top and par files for retinal?
rmv #20433 03/18/09 02:41 AM
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Thanks a lot rmv. I figured out how to patch lys with retinal.

Everything works fine now except that the retinal coordinates can't be read correctly (999999.00). I believe there might be something wrong with the following script or the attached reorganized pdb file, and I appreciate if you could help me find it out:

**************
open unit 1 read form name top_all27_prot_na.rtf
read rtf card unit 1
close unit 1

OPEN UNIT 11 read form NAME par_all27_prot_na.prm
READ PARA card UNIT 11
CLOSE UNIT 11

STREAM toppar_all22_prot_retinol.str




open unit 12 read form name br_no_ret.pdb
READ SEQUence PDB unit 12
close unit 12

GENErate brd SETUp first nter last cter



open unit 12 read form name ret.pdb
READ SEQUence PDB unit 12
close unit 12

GENErate ret SETUp first none last none



! GENERATE SCHIFF BASE
patch SCK0 brd 216 ret 301
AUTOgenerate ANGLes DIHEdrals



open unit 1 read form name br_no_ret.pdb
read coor pdb unit 1
close unit 1



open unit 1 read form name ret.pdb
read coor pdb append unit 1
close unit 1





ic param
ic build
hbuild sele hydrogen end


open unit 1 write form name br_unmin.pdb
write coor pdb unit 1
close unit 1

STOP

Attached Files
20783-RHO.zip (0 Bytes, 274 downloads)
Re: Where to get the top and par files for retinal?
Hailiang #20434 03/18/09 03:39 AM
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Check the output log file for messages, esp. when the coords are read.

Re: Where to get the top and par files for retinal?
rmv #20435 03/18/09 03:52 AM
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Just found that forgot to specify "setup" when "patching" retinal. Thanks anyway!

Re: Where to get the top and par files for retinal?
Hailiang #20436 03/19/09 09:05 PM
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Another problem:-(
After a series of IC and hbuild operations, the backbone coordinates were passed pretty well, but the sidechain coordinates were seriously messed. I wonder whether there is some problem the following scripts (see the above replies for the details):

***
Generate xx Setup
...
IC para
IC build
hbuild sele hydrogen end
...
Read coor...
*****

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