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?
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
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.
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.
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
