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#34968 05/07/15 06:38 PM
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talbers Offline OP
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I'd like to run MD on a protein that has an SAM (S-adenosyl methionine) ligand. The question has come up before (here: http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=1980) and people mentioned that there was a patch somewhere.

In CHARMM36 this patch SAM seems to have disappeared, at least I can't find it anywhere, and cationic tricoordinate sulphur isn't parametrized in cgenff or CHARMM. Does anyone have a topology and parameters?

Thanks

Last edited by talbers; 05/07/15 06:38 PM.
talbers #34969 05/07/15 08:26 PM
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rmv Offline
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The answer has not changed; perhaps you neglected to check the stream subdir, where many special additional molecules can be found. The SAM patch and required parameters still exist in the file toppar_all36_prot_na_combined.str


Rick Venable
computational chemist

talbers #38361 10/17/21 03:45 PM
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Hello,
I wanted to run MD simulation for a complex of 2 proteins with SAM as a co-factor of one protein. I used the SAM patch from the toppar_all36_prot_na_combined.str, but still I am unable to generate the psf file for my system.
I used the following input file for the generation of psf-

* Setting up nsp16 protein file
*

BOMLEVEL -19


OPEN UNIT 10 CARD READ NAME top_all36_prot.rtf
READ RTF CARD UNIT 10
CLOSE UNIT 10

OPEN UNIT 12 CARD READ NAME par_all36_prot.prm
READ PARA CARD UNIT 12
CLOSE UNIT 12


open read unit 60 card name "nsp16.pdb"
read sequ pdb unit 60
generate NS16 SETUP
REWIND UNIT 60
READ COOR PDB UNIT 60
CLOSE UNIT 60

IC FILL PRESERVE
IC PARAMETERS
IC BUILD
HBUILD



open read unit 61 card name "nsp10.pdb"
read sequ pdb unit 61
generate NS10 SETUP
REWIND UNIT 61
READ COOR PDB UNIT 61
CLOSE UNIT 61


IC FILL PRESERVE
IC PARAMETERS
IC BUILD
HBUILD


open read unit 62 card name "zinc.pdb"
read sequ pdb unit 62
generate ZINC SETUP
REWIND UNIT 62
READ COOR PDB UNIT 62
CLOSE UNIT 62

IC FILL PRESERVE
IC PARAMETERS
IC BUILD
HBUILD

open read unit 63 card name "sam.pdb"
read sequ pdb unit 63
generate SAM SETUP
patch SAM SAM 873 SETUP WARN
REWIND UNIT 63
READ COOR PDB UNIT 63
CLOSE UNIT 63

IC FILL PRESERVE
IC PARAMETERS
IC BUILD
HBUILD



open unit 1 write card name dimer_prepared.psf
write psf card unit 1

open unit 1 write card name dimer_preparedx.psf
write psf card xplor unit 1

open unit 1 write card name dimer_prepared.pdb
write coor pdb unit 1

open unit 1 write card name dimer_prepared.crd
write coor card unit 1

STOP

I get the following error. (output file attached)-
PRES SAM 1.00
**** ERROR in RTFRDR **** The atom type code, CN8B is unknown. The atom will be ignored.
ATOM C5' CN8B 0.03
**** ERROR in RTFRDR **** The atom type code, HN8 is unknown. The atom will be ignored.
ATOM H5' HN8 0.09
**** ERROR in RTFRDR **** The atom type code, HN8 is unknown. The atom will be ignored.
ATOM H5'' HN8 0.09
**** ERROR in RTFRDR **** The atom type code, CN7 is unknown. The atom will be ignored.
ATOM C3' CN7 0.14
**** ERROR in RTFRDR **** The atom type code, HN7 is unknown. The atom will be ignored.
ATOM H3' HN7 0.09
**** ERROR in RTFRDR **** The atom type code, ON5 is unknown. The atom will be ignored.
ATOM O3' ON5 -0.66
**** ERROR in RTFRDR **** The atom type code, HN5 is unknown. The atom will be ignored.
ATOM H3T HN5 0.43
**** WARNING from RTFRDR **** The total charge of the residue, SAM , 0.7900000,
does not equal the expected charge, 1.0000000.

Can anyone please help me out

Thanks

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ouptut_file.txt (52.58 KB, 126 downloads)
SHA1: 83939a82a165e1cc91ba4df64508770e9e14dfde
talbers #38362 10/17/21 04:15 PM
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rmv Offline
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This is appears to be more of a basic usage issue, and not a parameter issue. Many of the errors arise from initial attempt to read coordinates from a PDB file, which is NOT a native CHARMM format; it can be used for import, but often requires extra steps, esp. if there are any residues missing coordinates. Another issue is the use of BOMLEV -19, which is extreme, and ill-considered.

Suggested reading from the Script Archive: complex PDB input examples


Rick Venable
computational chemist

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talbers #38363 10/17/21 08:12 PM
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rmv Offline
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There is a parameter error of sorts, in that you've only read the protein topology and parameter files. From the comments in the file toppar_all36_prot_na_combined.str:

!Parent files that have to be read prior to streaming this file
!top_all36_prot.rtf
!par_all36_prot.prm
!top_all36_na.rtf
!par_all36_na.prm


Also, creating your own custom topology and parameter files by combining existing distributed files is not recommended for the general user. It is best to read them from a standard location, and not change those files in any way


Rick Venable
computational chemist

1 member likes this: MJ@SPPU

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