Dear all<br><br> I am doing simulation of DNA -protein complex using amber port with gromacs-4.0.3 . for this I have to make changes in my .pdb file a/c to entry in .rtp file of amber force field.<br>
<br>I have all possible changes but when I run the pdb2gmx command the error came like this-<br><br>Fatal error:<br>Atom O2 in residue DT 1 not found in rtp entry with 32 atoms<br> while sorting atoms<br><br>
and entry of atom in .rtp file like this-<br> P amber99_46 1.16590 1<br> O1P amber99_45 -0.77610 2<br> O2P amber99_45 -0.77610 3<br> O5' amber99_44 -0.49540 4<br> C5' amber99_11 -0.00690 5<br>
H5'1 amber99_19 0.07540 6<br> H5'2 amber99_19 0.07540 7<br> C4' amber99_11 0.16290 8<br> H4' amber99_19 0.11760 9<br> O4' amber99_44 -0.36910 10<br>
C1' amber99_11 0.06800 11<br> H1' amber99_20 0.18040 12<br> N1 amber99_40 -0.02390 13<br> C6 amber99_7 -0.22090 14<br> H6 amber99_23 0.26070 15<br> C5 amber99_7 0.00250 16<br>
C7 amber99_11 -0.22690 17<br> H71 amber99_18 0.07700 18<br> H72 amber99_18 0.07700 19<br> H73 amber99_18 0.07700 20<br> C4 amber99_2 0.51940 21<br> O4 amber99_41 -0.55630 22<br>
N3 amber99_35 -0.43400 23<br> H3 amber99_17 0.34200 24<br> C2 amber99_2 0.56770 25<br> O amber99_41 -0.58810 26<br> C3' amber99_11 0.07130 27<br> H3' amber99_19 0.09850 28<br>
C2' amber99_11 -0.08540 29<br> H2'1 amber99_18 0.07180 30<br> H2'2 amber99_18 0.07180 31<br> O3' amber99_44 -0.52320 32<br><br>So, can anyone suggest me at the place 02 what name I can change in my .pdb file.<br>
<br>Thanking you<br>Nitu sharma<br><br>