Dear gmx users, I have just realized, at the end of a molecular dynamics simulation, that I had in my .gro file to aminoacids with the same number. This happened cause in my pdb file, what was supposed to be residue 53, was instead 52A (due to an insertion of Lys in that position, compared to other homologs). Those are the lines in the .pdb I am talking about.
ATOM 482 HA ASN A 52 11.594 -3.380 37.114 1.00 0.00 H ATOM 483 HB3 ASN A 52 10.188 -5.588 35.526 1.00 0.00 H ATOM 484 HB2 ASN A 52 11.571 -5.800 36.555 1.00 0.00 H ATOM 485 HD21 ASN A 52 7.924 -5.965 38.224 1.00 0.00 H ATOM 486 HD22 ASN A 52 8.207 -5.978 36.494 1.00 0.00 H ATOM 487 N LYS A 52A 11.898 -2.478 34.227 1.00 26.03 N ATOM 488 CA LYS A 52A 12.656 -2.134 33.020 1.00 26.03 C ATOM 489 C LYS A 52A 12.428 -3.160 31.890 1.00 25.58 C ATOM 490 O LYS A 52A 13.333 -3.399 31.090 1.00 25.54 O ATOM 491 CB LYS A 52A 14.147 -1.837 33.318 1.00 26.46 C So basically in the .gro file the residue 52 is composed by the ASN 52 and LYS 52. The question is if this can constitute a problem for the simulation? It seems that everything went smooth and I got no error, but I would like to double check.. Thanks for your time, Davide -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
