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Thanks again, <br><br>You were right, it was a misaligned pdb file :).<br><br>However I now get an error when I use grompp:<br><br>ERROR 1 [file newoxi.noNaCl_DNA.itp, line 1381]:<br>&nbsp; No default Bond types<br><br><br>ERROR 2 [file newoxi.noNaCl_DNA.itp, line 4462]:<br>&nbsp; No default Angle types<br><br><br>ERROR 3 [file newoxi.noNaCl_DNA.itp, line 4464]:<br>&nbsp; No default Angle types<br><br><br>ERROR 4 [file newoxi.noNaCl_DNA.itp, line 6919]:<br>&nbsp; No default Improper Dih. types<br><br>My assumption is that I have not set the angles and dihedrals properly but have rechecked the rtp entry and all seems to be correct.<br><br>Once Again thank you for helping out a gromacs newbie.<br><br><br><br>&gt; Date: Thu, 3 Feb 2011 20:43:24 -0500<br>&gt; From: jalemkul@vt.edu<br>&gt; To: gmx-users@gromacs.org<br>&gt; Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield<br>&gt; <br>&gt; <br>&gt; <br>&gt; william Stebbeds wrote:<br>&gt; &gt; Thanks for the reply,<br>&gt; &gt; <br>&gt; &gt; ffamber99sb.rtp entry:<br>&gt; &gt; [ DGO ]<br>&gt; &gt;  [ atoms ]<br>&gt; &gt;      P    amber99_46    1.16590     1<br>&gt; &gt;    O1P    amber99_45   -0.77610     2<br>&gt; &gt;    O2P    amber99_45   -0.77610     3<br>&gt; &gt;    O5'    amber99_44   -0.49540     4<br>&gt; &gt;    C5'    amber99_11   -0.00690     5<br>&gt; &gt;   H5'1    amber99_19    0.07540     6<br>&gt; &gt;   H5'2    amber99_19    0.07540     7<br>&gt; &gt;    C4'    amber99_11    0.16290     8<br>&gt; &gt;    H4'    amber99_19    0.11760     9<br>&gt; &gt;    O4'    amber99_44   -0.36910    10<br>&gt; &gt;    C1'    amber99_11    0.03580    11<br>&gt; &gt;    H1'    amber99_20    0.17460    12<br>&gt; &gt;     N9    amber99_40    0.05770    13<br>&gt; &gt;     C8    amber99_6     0.07360    14<br>&gt; &gt;     O8    amber99_44   -0.36910    15<br>&gt; &gt;     N7    amber99_36   -0.57250    16<br>&gt; &gt;     C5    amber99_4     0.19910    17<br>&gt; &gt;     C6    amber99_2     0.49180    18<br>&gt; &gt;     O6    amber99_41   -0.56990    19<br>&gt; &gt;     N1    amber99_35   -0.50530    20<br>&gt; &gt;     H1    amber99_17    0.35200    21<br>&gt; &gt;     C2    amber99_3     0.74320    22<br>&gt; &gt;     N2    amber99_38   -0.92300    23<br>&gt; &gt;    H21    amber99_17    0.42350    24<br>&gt; &gt;    H22    amber99_17    0.42350    25<br>&gt; &gt;     N3    amber99_37   -0.66360    26<br>&gt; &gt;     C4    amber99_4     0.18140    27<br>&gt; &gt;    C3'    amber99_11    0.07130    28<br>&gt; &gt;    H3'    amber99_19    0.09850    29<br>&gt; &gt;    C2'    amber99_11   -0.08540    30<br>&gt; &gt;   H2'1    amber99_18    0.07180    31<br>&gt; &gt;   H2'2    amber99_18    0.07180    32<br>&gt; &gt;    O3'    amber99_44   -0.52320    33<br>&gt; &gt;   [ bonds ]<br>&gt; &gt;      P   O1P<br>&gt; &gt;      P   O2P<br>&gt; &gt;      P   O5'<br>&gt; &gt;    O5'   C5'<br>&gt; &gt;    C5'  H5'1<br>&gt; &gt;    C5'  H5'2<br>&gt; &gt;    C5'   C4'<br>&gt; &gt;    C4'   H4'<br>&gt; &gt;    C4'   O4'<br>&gt; &gt;    C4'   C3'<br>&gt; &gt;    O4'   C1'<br>&gt; &gt;    C1'   H1'<br>&gt; &gt;    C1'    N9<br>&gt; &gt;    C1'   C2'<br>&gt; &gt;     N9    C8<br>&gt; &gt;     N9    C4<br>&gt; &gt;     C8    O8<br>&gt; &gt;     C8    N7<br>&gt; &gt;     N7    C5<br>&gt; &gt;     C5    C6<br>&gt; &gt;     C5    C4<br>&gt; &gt;     C6    O6<br>&gt; &gt;     C6    N1<br>&gt; &gt;     N1    H1<br>&gt; &gt;     N1    C2<br>&gt; &gt;     C2    N2<br>&gt; &gt;     C2    N3<br>&gt; &gt;     N2   H21<br>&gt; &gt;     N2   H22<br>&gt; &gt;     N3    C4<br>&gt; &gt;    C3'   H3'<br>&gt; &gt;    C3'   C2'<br>&gt; &gt;    C3'   O3'<br>&gt; &gt;    C2'  H2'1<br>&gt; &gt;    C2'  H2'2<br>&gt; &gt;   -O3'     P<br>&gt; &gt;  [ dihedrals ]<br>&gt; &gt;    O4' C1' N9 C4   proper_X_CT_N*_X<br>&gt; &gt;    C1' N9  C8 O8   proper_X_CK_N*_X<br>&gt; &gt;    C1' N9  C8 N7   proper_X_CK_N*_X<br>&gt; &gt;    C1' N9  C4 C5   proper_X_CB_N*_X<br>&gt; &gt;    C1' N9  C4 N3   proper_X_CB_N*_X<br>&gt; &gt;    H1' C1' N9 C8   proper_X_CT_N*_X<br>&gt; &gt;    H1' C1' N9 C4   proper_X_CT_N*_X<br>&gt; &gt;    C8  N9  C4 C5   proper_X_CB_N*_X<br>&gt; &gt;    C8  N9  C4 N3   proper_X_CB_N*_X<br>&gt; &gt;    C5  C6  N1 H1   proper_X_C_NA_X<br>&gt; &gt;    C5  C6  N1 C2   proper_X_C_NA_X<br>&gt; &gt;    C6  N1  C2 N2   proper_X_CA_NA_X<br>&gt; &gt;    C6  N1  C2 N3   proper_X_CA_NA_X<br>&gt; &gt;    O6  C6  N1 H1   proper_X_C_NA_X<br>&gt; &gt;    O6  C6  N1 C2   proper_X_C_NA_X<br>&gt; &gt;    N1  C2  N3 C4   proper_X_CA_NC_X<br>&gt; &gt;    H1  N1  C2 N2   proper_X_CA_NA_X<br>&gt; &gt;    H1  N1  C2 N3   proper_X_CA_NA_X<br>&gt; &gt;    N2  C2  N3 C4   proper_X_CA_NC_X<br>&gt; &gt;    H8  C8  N7 C5   proper_X_CK_NB_X<br>&gt; &gt;    N9  C8  N7 C5   proper_X_CK_NB_X<br>&gt; &gt;    H8  C8  N9 C4   proper_X_CK_N*_X<br>&gt; &gt;    N7  C8  N9 C4   proper_X_CK_N*_X<br>&gt; &gt;    O4' C1' C2' H2'1   proper_H_CT_CT_O<br>&gt; &gt;    O4' C1' C2' H2'2   proper_H_CT_CT_O<br>&gt; &gt;    O3' C3' C2' H2'1   proper_H_CT_CT_O<br>&gt; &gt;    O3' C3' C2' H2'2   proper_H_CT_CT_O<br>&gt; &gt;  [ impropers ]<br>&gt; &gt;     C4    C8    N9   C1'  nucleic_imp_10<br>&gt; &gt;     C5    N1    C6    O6<br>&gt; &gt;     C6    C2    N1    H1  nucleic_imp_10<br>&gt; &gt;     C2   H21    N2   H22<br>&gt; &gt;     N9    N7    C8    O8<br>&gt; &gt;     N2    N1    C2    N3  nucleic_imp_11<br>&gt; &gt; <br>&gt; &gt; DGO was also added to residuetypes.dat. hdb file was also updated, as <br>&gt; &gt; was dna.rtp within amber99sb.ff.<br>&gt; &gt; <br>&gt; &gt; The problem is not a simple missing bond, as when the structure goes <br>&gt; &gt; through pdb2gmx, the new nucleotide appears on the other side of the <br>&gt; &gt; pbc, in a straight line (i.e. without form).<br>&gt; &gt; <br>&gt; <br>&gt; As in, the atoms of DGO are visually a straight line?  That would be a <br>&gt; consequence of an incorrectly-formatted input file.  If you're using a .pdb <br>&gt; file, it's fixed-format, so any incorrect spacing will screw up the coordinates.<br>&gt; <br>&gt; To clarify, are you missing a bond, as your first message would imply?  I can <br>&gt; see how you might be missing bonds; your residue definition doesn't specify a <br>&gt; bond to the next nucleotide (i.e. "O3' +P"), although if it's a 3' ending <br>&gt; nucleotide, this wouldn't apply.  If it's an internal residue, you may also be <br>&gt; missing necessary dihedral definitions as well.<br>&gt; <br>&gt; -Justin<br>&gt; <br>&gt; &gt; Thanks<br>&gt; &gt; <br>&gt; &gt; Will<br>&gt; &gt; <br>&gt; &gt;  &gt; Date: Thu, 3 Feb 2011 16:07:42 -0500<br>&gt; &gt;  &gt; From: jalemkul@vt.edu<br>&gt; &gt;  &gt; To: gmx-users@gromacs.org<br>&gt; &gt;  &gt; Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield<br>&gt; &gt;  &gt;<br>&gt; &gt;  &gt;<br>&gt; &gt;  &gt;<br>&gt; &gt;  &gt; william Stebbeds wrote:<br>&gt; &gt;  &gt; &gt; Hello,<br>&gt; &gt;  &gt; &gt;<br>&gt; &gt;  &gt; &gt; I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the<br>&gt; &gt;  &gt; &gt; amber99sb force field. This is a simple modification of the H8 <br>&gt; &gt; hydrogen<br>&gt; &gt;  &gt; &gt; on a guanine to an oxygen atom. I have followed the instructions on <br>&gt; &gt; the<br>&gt; &gt;  &gt; &gt; gromacs site on adding residues.<br>&gt; &gt;  &gt; &gt;<br>&gt; &gt;  &gt; &gt; However the new nucleotide will not work, it will not attach to the<br>&gt; &gt;  &gt; &gt; adjacent nucleotides in the sequence.<br>&gt; &gt;  &gt; &gt;<br>&gt; &gt;  &gt;<br>&gt; &gt;  &gt; So a bond is missing?<br>&gt; &gt;  &gt;<br>&gt; &gt;  &gt; &gt; Any help would be very much appreciated, if any more information is<br>&gt; &gt;  &gt; &gt; required please let me know.<br>&gt; &gt;  &gt; &gt;<br>&gt; &gt;  &gt;<br>&gt; &gt;  &gt; A lot more information is needed, at the very least, your .rtp entry.<br>&gt; &gt;  &gt;<br>&gt; &gt;  &gt; -Justin<br>&gt; &gt;  &gt;<br>&gt; &gt;  &gt; &gt; Best Regards<br>&gt; &gt;  &gt; &gt;<br>&gt; &gt;  &gt; &gt; William Stebbeds<br>&gt; &gt;  &gt; &gt; Cranfield University<br>&gt; &gt;  &gt; &gt; UK<br>&gt; &gt;  &gt; &gt;<br>&gt; &gt;  &gt;<br>&gt; &gt;  &gt; --<br>&gt; &gt;  &gt; ========================================<br>&gt; &gt;  &gt;<br>&gt; &gt;  &gt; Justin A. Lemkul<br>&gt; &gt;  &gt; Ph.D. Candidate<br>&gt; &gt;  &gt; ICTAS Doctoral Scholar<br>&gt; &gt;  &gt; MILES-IGERT Trainee<br>&gt; &gt;  &gt; Department of Biochemistry<br>&gt; &gt;  &gt; Virginia Tech<br>&gt; &gt;  &gt; Blacksburg, VA<br>&gt; &gt;  &gt; jalemkul[at]vt.edu | (540) 231-9080<br>&gt; &gt;  &gt; http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>&gt; &gt;  &gt;<br>&gt; &gt;  &gt; ========================================<br>&gt; &gt;  &gt; --<br>&gt; &gt;  &gt; gmx-users mailing list gmx-users@gromacs.org<br>&gt; &gt;  &gt; http://lists.gromacs.org/mailman/listinfo/gmx-users<br>&gt; &gt;  &gt; Please search the archive at <br>&gt; &gt; http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>&gt; &gt;  &gt; Please don't post (un)subscribe requests to the list. Use the<br>&gt; &gt;  &gt; www interface or send it to gmx-users-request@gromacs.org.<br>&gt; &gt;  &gt; Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>&gt; &gt; <br>&gt; <br>&gt; -- <br>&gt; ========================================<br>&gt; <br>&gt; Justin A. Lemkul<br>&gt; Ph.D. Candidate<br>&gt; ICTAS Doctoral Scholar<br>&gt; MILES-IGERT Trainee<br>&gt; Department of Biochemistry<br>&gt; Virginia Tech<br>&gt; Blacksburg, VA<br>&gt; jalemkul[at]vt.edu | (540) 231-9080<br>&gt; http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>&gt; <br>&gt; ========================================<br>&gt; -- <br>&gt; gmx-users mailing list    gmx-users@gromacs.org<br>&gt; http://lists.gromacs.org/mailman/listinfo/gmx-users<br>&gt; Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>&gt; Please don't post (un)subscribe requests to the list. Use the <br>&gt; www interface or send it to gmx-users-request@gromacs.org.<br>&gt; Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>                                               </body>
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