Hi All I have built DNA with NAB in AMBER and it provide names as D*, D*3, D*5 (where * = A,T,G,C) and want to use charmm27 in gromacs. The charmm27.ff/dna.rtp does not have D*5 or D*3 and has only D* residues, so I renamed D*5 or D*3 to just corresponding D* residues. The output pdb with pdb2gmx as looked in vmd is fine but why? As far as I know in gromacs the sequence of loading structure should match rtp file. So I have following two queries:
1) Here is comparison for DA residue (non-terminal): #My #charmm27/dna.rtp P P OP1 O1P <still ok as gromacs will rename atom; No problem OP2 O2P <still ok as gromacs will rename atom O5' O5' C5' C5' H5' H5'1 <still ok as gromacs will rename atom H5'' H5'2 <still ok as gromacs will rename atom C4' C4' H4' H4' O4' O4' C1' C1' H1' H1' N9 N9 C8 C5 < difference starts H8 N7 N7 C8 C5 H8 C6 N1 N6 C2 H61 H2 H62 N3 N1 C4 C2 C6 H2 N6 N3 H61 C4 H62 C3' C2' H3' H2'1 C2' H2'2 H2' C3' H2'' H3' O3' O3' 2) Also I noticed as there are no D*3 or D*5 exist in dna.rtp, somehow gromacs add/deletes atoms from dna.c.tdb or dna.n.tdb files and finally I get correct atoms. But same here also atom sequence is not same! best regards Jiom -- 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.