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<p class=MsoNormal> <span class=st1><span lang=EN-US style='font-family:
"Arial","sans-serif";color:#222222'>Dear Gromacs Users,<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'>
I m trying to simulate a <b>DNA</b> structure with <b>amber03 force field</b>. However,
when I give first command of pdb2gmx.<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'>Following error comes:<o:p></o:p></span></span></p>
<p class=MsoNormal><b><span lang=EN-US>Fatal error:</span></b><span class=st1><b><span
lang=EN-US style='font-family:"Arial","sans-serif";color:#222222'> Atom O5' not
found in residue seq.nr. 1 while adding atom.<o:p></o:p></span></b></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'>As O5’ is present in DA nucleic acid. So,I checked <b>DNA.rtp</b>
file and nomenclature of DA, DT and all other nucleic acid residues is same for
both .pdb and .rtp file.<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'>Plz plz guide me how to solve this problem.<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><b><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'>Following is my .rtp file for DA<o:p></o:p></span></b></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'>[ DA ]<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> [ atoms ]<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> P
P
1.16590 1<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> O1P
O2
-0.77610 2<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> O2P
O2
-0.77610 3<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> O5'
OS
-0.49540 4<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C5'
CT
-0.00690 5<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> H5'1
H1
0.07540 6<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> H5'2
H1
0.07540 7<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C4'
CT
0.16290 8<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> H4'
H1 0.11760
9<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> O4'
OS
-0.36910 10<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C1'
CT
0.04310 11<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> H1'
H2
0.18380 12<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N9
N*
-0.02680 13<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C8
CK
0.16070 14<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> H8
H5
0.18770 15<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N7
NB -0.61750
16<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C5
CB
0.07250 17<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C6
CA
0.68970 18<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N6
N2
-0.91230 19<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> H61
H
0.41670 20<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> H62
H
0.41670 21<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N1
NC
-0.76240 22<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C2 CQ
0.57160 23<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> H2
H5
0.05980 24<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N3
NC
-0.74170 25<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C4
CB
0.38000 26<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C3'
CT
0.07130 27<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> H3'
H1
0.09850 28<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C2'
CT
-0.08540 29<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> H2'1
HC
0.07180 30<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> H2'2
HC
0.07180 31<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> O3'
OS
-0.52320 32<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> [ bonds ]<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> P O1P<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> P O2P<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> P O5'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> O5' C5'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C5' H5'1<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C5' H5'2<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C5' C4'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C4' H4'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C4' O4'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C4' C3'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> O4' C1'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C1' H1'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C1' N9<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C1' C2'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N9 C8<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N9 C4<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C8 H8<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C8 N7<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N7 C5<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C5 C6<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C5 C4<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C6 N6<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C6 N1<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N6 H61<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N6 H62<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N1 C2<o:p></o:p></span></span></p>
<p class=MsoNormal style='text-indent:15.0pt'><span class=st1><span lang=EN-US
style='font-family:"Arial","sans-serif";color:#222222'>C2 H2<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C2 N3<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N3 C4<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C3' H3'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C3' C2'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C3' O3'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C2' H2'1<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C2' H2'2<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> -O3' P<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> [ impropers ]<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C4 C8
N9 C1'<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C6 H61
N6 H62<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N9 N7
C8 H8<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> N1 N3
C2 H2<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'> C5 N6
C6 N1<o:p></o:p></span></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'><o:p> </o:p></span></span></p>
<p class=MsoNormal><span class=st1><b><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'>Following is DA part of my pdb file:<o:p></o:p></span></b></span></p>
<p class=MsoNormal><span class=st1><span lang=EN-US style='font-family:"Arial","sans-serif";
color:#222222'><o:p> </o:p></span></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM
28 P DA E 10
-24.026 32.156 -43.818
1.00180.08 P<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 29
O1P DA E 10 -23.715 31.139
-42.788 1.00173.83 O<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 30
O2P DA E 10 -25.435 32.499
-44.114 1.00161.01 O<o:p></o:p></span></p>
<p class=MsoNormal><b><span lang=EN-US>ATOM 31
O5' DA E 10 -23.255 33.516
-43.475 1.00127.88 O<o:p></o:p></span></b></p>
<p class=MsoNormal><span lang=EN-US>ATOM 32
C5' DA E 10 -23.498 34.194
-42.247
1.00107.59 C<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 33 C4'
DA E 10 -23.169 33.299 -41.066
1.00102.86 C<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 34
O4' DA E 10 -21.825 32.777
-41.221 1.00
93.42 O<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 35
C3' DA E 10 -23.220 33.983
-39.705
1.00102.18 C<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 36
O3' DA E 10 -23.829 33.119
-38.754 1.00
83.31 O<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 37
C2' DA E 10 -21.755 34.244
-39.363
1.00102.50 C<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 38
C1' DA E 10 -21.012 33.153
-40.128 1.00
81.75 C<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 39
N9 DA E 10 -19.721 33.596
-40.647 1.00
82.20 N<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 40
C8 DA E 10 -19.495 34.603
-41.544 1.00
94.12 C<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 41
N7 DA E 10 -18.227 34.783
-41.832
1.00102.29 N<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 42
C5 DA E 10 -17.576 33.827
-41.070 1.00 96.10
C<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 43
C6 DA E 10 -16.215 33.496
-40.924 1.00
87.15 C<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 44
N6 DA E 10 -15.230 34.125
-41.572 1.00
84.12 N<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 45
N1 DA E 10 -15.903 32.488
-40.082 1.00
75.71 N<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 46
C2 DA E 10 -16.891 31.860
-39.434 1.00
80.51 C<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 47
N3 DA E 10 -18.203 32.081
-39.490 1.00
91.21 N<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 48
C4 DA E 10 -18.482 33.087
-40.334 1.00
96.39 C<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 49 H5'1
DA E 10 -22.876 35.088 -42.203
1.00105.06 H<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 50
H5'2 DA E 10 -24.549 34.479
-42.198
1.00105.06 H<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 51
H4' DA E 10 -23.867 32.462
-41.060
1.00105.06 H<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 52
H3' DA E 10 -23.768 34.923
-39.772
1.00105.06 H<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 53
H2'1 DA E 10 -21.447 35.234
-39.699
1.00105.06 H<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 54
H2'2 DA E 10 -21.583 34.154
-38.290
1.00105.06 H<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 55
H1' DA E 10 -20.863 32.292 -39.476
1.00105.06 H<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 56
H8 DA E 10 -20.295 35.202
-41.980
1.00105.06 H<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 57
H61 DA E 10 -15.458 34.926
-42.244
1.00105.06 H<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 58
H62 DA E 10 -14.214 33.827
-41.419
1.00105.06 H<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>ATOM 59
H2 DA E 10 -16.579 31.056
-38.768
1.00105.06 H<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>I will be very thankful. <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Best regards<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>mahreen<o:p></o:p></span></p>
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