GROMACS version:
GROMACS modification: Yes/No
how to add topology of cofactor (or) non standard residue such as LLP( N’-PYRIDOXYL-LYSINE-5 '-MONOPHOSPHATE) with protein. charmm36 force field unable to do so
I just answered a similar question (with recommended links). See Topology creation for non-standard amino acid residues.
thanku sir for your suggestion
GROMACS version: 2021.4
GROMACS modification: No
hello sir,
i have tried as per suggested by the link to merge the rtp file of LLP69 with charmm36forcefield containing aminoacids.rtp file but stll i’m getting fatal error.
“The residues in the chain GLU7–PRO427 do not have a consistent type. The
first residue has type ‘Protein’, while residue LLP69 is of type ‘Other’.
Either there is a mistake in your chain, or it includes nonstandard residue
names that have not yet been added to the residuetypes.dat file in the GROMACS
library directory. If there are other molecules such as ligands, they should
not have the same chain ID as the adjacent protein chain since it’s a separate
molecule.”
please suggest me how to overcome it.
I guess you’ll have to go through the error message carefully and make sure that you address the issues. If LLP69 is not a protein residue it cannot be in the same chain as a protein.
LLP69 is a cofactor present in protein as because the protein is LLP- dependent enzyme, so that for md simulation i need to keep the LLP with in the protein residue attached with lysine amino acid.
Yes, but is it part of the protein itself (a protein residue) or is it separate, i.e., in a separate chain?
it is a part of protein and attached with lysine residue and attached with protein chain.
ATOM 499 O ALA A 67 8.772 7.783 52.277 1.00 5.12 O
ATOM 500 CB ALA A 67 8.655 10.751 52.000 1.00 5.12 C
ATOM 501 N VAL A 68 10.972 7.964 52.445 1.00 5.12 N
ATOM 502 CA VAL A 68 11.225 6.600 52.889 1.00 8.39 C
ATOM 503 C VAL A 68 10.331 6.151 54.077 1.00 8.27 C
ATOM 504 O VAL A 68 9.954 4.993 54.209 1.00 5.12 O
ATOM 505 CB VAL A 68 12.713 6.450 53.307 1.00 5.12 C
ATOM 506 CG1 VAL A 68 12.984 5.117 54.037 1.00 5.12 C
ATOM 507 CG2 VAL A 68 13.645 6.612 52.084 1.00 5.12 C
HETATM 508 N LLP A 69 9.971 7.101 54.969 1.00 5.12 N
HETATM 509 CA LLP A 69 9.260 6.807 56.180 1.00 5.12 C
HETATM 510 C LLP A 69 7.835 6.288 55.880 1.00 8.33 C
HETATM 511 O LLP A 69 7.375 5.576 56.745 1.00 5.21 O
HETATM 512 O3 LLP A 69 7.337 15.015 56.756 1.00 10.55 O
HETATM 513 C4 LLP A 69 6.517 13.766 54.813 1.00 12.57 C
HETATM 514 C4’ LLP A 69 5.897 12.755 55.666 1.00 23.29 C
HETATM 515 C5 LLP A 69 6.533 13.672 53.385 1.00 11.01 C
HETATM 516 C6 LLP A 69 7.289 14.539 52.643 1.00 5.58 C
HETATM 517 C5’ LLP A 69 5.723 12.503 52.785 1.00 5.12 C
HETATM 518 OP4 LLP A 69 4.364 12.860 52.863 1.00 5.12 O
HETATM 519 P LLP A 69 3.167 12.059 52.041 1.00 6.30 P
HETATM 520 OP1 LLP A 69 1.924 12.584 52.630 1.00 7.90 O1-
HETATM 521 OP2 LLP A 69 3.342 10.559 52.256 1.00 5.12 O1-
HETATM 522 OP3 LLP A 69 3.528 12.484 50.702 1.00 5.12 O
HETATM 523 N1 LLP A 69 7.981 15.507 53.290 1.00 5.12 N
HETATM 524 C2 LLP A 69 8.006 15.671 54.602 1.00 5.12 C
HETATM 525 CB LLP A 69 8.973 7.938 57.172 1.00 5.12 C
HETATM 526 CG LLP A 69 8.106 9.086 56.689 1.00 8.11 C
HETATM 527 CD LLP A 69 7.943 10.252 57.676 1.00 14.67 C
HETATM 528 CE LLP A 69 6.683 11.079 57.464 1.00 17.91 C
HETATM 529 NZ LLP A 69 6.701 12.054 56.414 1.00 8.31 N
HETATM 530 C2’ LLP A 69 8.803 16.832 55.227 1.00 10.20 C
HETATM 531 C3 LLP A 69 7.266 14.765 55.404 1.00 15.01 C
HETATM 532 HN LLP A 69 10.228 8.119 54.762 1.00 8.79 H
HETATM 533 HA LLP A 69 9.802 6.023 56.709 1.00 8.79 H
HETATM 534 H3 LLP A 69 6.379 15.240 57.122 1.00 8.79 H
HETATM 535 H4’ LLP A 69 4.819 12.596 55.676 1.00 8.79 H
HETATM 536 H6 LLP A 69 7.333 14.452 51.557 1.00 8.79 H
HETATM 537 1H5’ LLP A 69 6.009 12.345 51.745 1.00 8.79 H
HETATM 538 2H5’ LLP A 69 5.904 11.592 53.355 1.00 8.79 H
HETATM 539 HB1 LLP A 69 8.479 7.496 58.037 1.00 8.79 H
HETATM 540 HB2 LLP A 69 9.932 8.358 57.476 1.00 8.79 H
HETATM 541 HG1 LLP A 69 8.549 9.480 55.774 1.00 8.79 H
HETATM 542 HG2 LLP A 69 7.114 8.689 56.471 1.00 8.79 H
HETATM 543 HD1 LLP A 69 7.917 9.843 58.686 1.00 8.79 H
HETATM 544 HD2 LLP A 69 8.805 10.911 57.572 1.00 8.79 H
HETATM 545 HE1 LLP A 69 5.869 10.386 57.252 1.00 8.79 H
HETATM 546 HE2 LLP A 69 6.478 11.606 58.396 1.00 8.79 H
HETATM 547 1H2’ LLP A 69 8.702 16.800 56.312 1.00 8.79 H
HETATM 548 2H2’ LLP A 69 8.416 17.781 54.855 1.00 8.79 H
HETATM 549 3H2’ LLP A 69 9.855 16.738 54.957 1.00 8.79 H
ATOM 550 N CYS A 70 7.204 6.608 54.741 1.00 5.12 N
ATOM 551 CA CYS A 70 5.914 6.161 54.321 1.00 5.12 C
ATOM 552 C CYS A 70 5.829 4.624 54.235 1.00 5.12 C
ATOM 553 O CYS A 70 4.859 4.072 54.744 1.00 5.32 O
ATOM 554 CB CYS A 70 5.583 6.660 52.915 1.00 6.41 C
ATOM 555 SG CYS A 70 3.853 6.339 52.421 1.00 5.12 S
i also tried to change the chain LLP69 A to LLP69 B to treat LLP as other chain but again im getting some other error:
Fatal error:
Atom -C not found in residue LLP 69, rtp entry LLP while adding hydrogens
Then you must make it a Protein, not Other. Have you looked at the residuetypes.dat file, as suggested in the error message?
yes sir, i have changed the residuetypes .dat file and to make LLP as protein
i got it sir, actually i have changed the residuetypes.dat in force field file instead of gromacs directory. now the topology is generate along with cofactor…
thank you for understanding and support