My complete input file is<br><br>ATOM 1 N CCMT 1 -2.521 -2.813 2.083 0.00 0.00<br>ATOM 2 CA CCMT 1 -2.925 -1.739 1.166 0.00 0.00<br>ATOM 3 C CCMT 1 -1.711 -0.842 0.859 0.00 0.00<br>
ATOM 4 CB CCMT 1 -4.034 -0.895 1.821 0.00 0.00<br>ATOM 5 SG CCMT 1 -4.523 0.408 0.710 0.00 0.00<br>ATOM 6 SD CCMT 1 -5.981 1.512 1.567 0.00 0.00<br>ATOM 7 CE CCMT 1 -7.394 0.480 1.895 0.00 0.00<br>
ATOM 8 CZ CCMT 1 -6.988 -0.662 2.846 0.00 0.00<br>ATOM 9 CH CCMT 1 -7.604 -2.072 2.895 0.00 0.00<br>ATOM 10 CH1 CCMT 1 -8.797 -2.090 3.869 0.00 0.00<br>ATOM 11 CH2 CCMT 1 -8.096 -2.574 1.525 0.00 0.00<br>
ATOM 12 CI CCMT 1 -5.986 -1.995 4.476 0.00 0.00<br>ATOM 13 CI1 CCMT 1 -4.582 -2.406 4.958 0.00 0.00<br>ATOM 14 CI2 CCMT 1 -6.931 -2.001 5.692 0.00 0.00<br>ATOM 15 CK CCMT 1 -6.018 -0.615 3.792 0.00 0.00<br>
ATOM 16 NT1 CCMT 1 -6.486 -2.876 3.411 0.00 0.00<br>ATOM 17 OC1 CCMT 1 -0.511 -1.346 0.867 0.00 0.00<br>ATOM 18 OC2 CCMT 1 -1.885 0.420 0.592 0.00 0.00<br>ATOM 19 OT1 CCMT 1 -6.836 -4.122 3.830 0.00 0.00<br>
ATOM 20 H CCMT 1 -1.801 -3.362 1.658 0.00 0.00<br>ATOM 21 HA CCMT 1 -3.292 -2.165 0.256 0.00 0.00<br>ATOM 22 HB1 CCMT 1 -4.878 -1.518 2.033 0.00 0.00<br>ATOM 23 HB2 CCMT 1 -3.668 -0.468 2.731 0.00 0.00<br>
ATOM 24 HE1 CCMT 1 -7.754 0.067 0.976 0.00 0.00<br>ATOM 25 HE2 CCMT 1 -8.165 1.065 2.350 0.00 0.00<br>ATOM 26 HH11 CCMT 1 -9.175 -3.088 3.952 0.00 0.00<br>ATOM 27 HH21 CCMT 1 -8.875 -1.932 1.170 0.00 0.00<br>
ATOM 28 HH12 CCMT 1 -8.477 -1.749 4.832 0.00 0.00<br>ATOM 29 HH22 CCMT 1 -7.283 -2.566 0.829 0.00 0.00<br>ATOM 30 HH13 CCMT 1 -9.567 -1.446 3.500 0.00 0.00<br>ATOM 31 HH23 CCMT 1 -8.471 -3.571 1.624 0.00 0.00<br>
ATOM 32 HI11 CCMT 1 -4.241 -1.712 5.697 0.00 0.00<br>ATOM 33 HI21 CCMT 1 -6.956 -2.982 6.119 0.00 0.00<br>ATOM 34 HI12 CCMT 1 -4.624 -3.387 5.383 0.00 0.00<br>ATOM 35 HI22 CCMT 1 -6.577 -1.303 6.422 0.00 0.00<br>
ATOM 36 HI13 CCMT 1 -3.906 -2.405 4.128 0.00 0.00<br>ATOM 37 HI23 CCMT 1 -7.915 -1.722 5.380 0.00 0.00<br>ATOM 38 HK CCMT 1 -5.391 0.221 4.019 0.00 0.00<br>ATOM 39 N NARG 2 -4.657 -5.920 2.257 0.00 0.00<br>
ATOM 40 CA NARG 2 -3.476 -5.161 2.694 0.00 0.00<br>ATOM 41 C NARG 2 -3.680 -3.668 2.378 0.00 0.00<br>ATOM 42 O NARG 2 -4.839 -3.179 2.371 0.00 0.00<br>ATOM 43 CB NARG 2 -2.230 -5.679 1.952 0.00 0.00<br>
ATOM 44 CG NARG 2 -0.992 -4.885 2.410 0.00 0.00<br>ATOM 45 CZ NARG 2 2.459 -4.459 1.265 0.00 0.00<br>ATOM 46 CD NARG 2 0.254 -5.404 1.668 0.00 0.00<br>ATOM 47 NE NARG 2 1.436 -4.648 2.106 0.00 0.00<br>
ATOM 48 NH1 NARG 2 2.406 -4.958 0.025 0.00 0.00<br>ATOM 49 NH2 NARG 2 3.535 -3.771 1.664 0.00 0.00<br>ATOM 50 HA NARG 2 -3.341 -5.287 3.748 0.00 0.00<br>ATOM 51 HB1 NARG 2 -2.089 -6.716 2.172 0.00 0.00<br>
ATOM 52 HB2 NARG 2 -2.365 -5.552 0.898 0.00 0.00<br>ATOM 53 HG1 NARG 2 -1.132 -3.847 2.190 0.00 0.00<br>ATOM 54 HG2 NARG 2 -0.858 -5.011 3.464 0.00 0.00<br>ATOM 55 HD1 NARG 2 0.393 -6.442 1.888 0.00 0.00<br>
ATOM 56 HD2 NARG 2 0.120 -5.278 0.614 0.00 0.00<br>ATOM 57 HE NARG 2 1.475 -4.274 3.033 0.00 0.00<br>ATOM 58 HH11 NARG 2 1.602 -5.472 -0.274 0.00 0.00<br>ATOM 59 HH21 NARG 2 3.574 -3.398 2.591 0.00 0.00<br>
ATOM 60 HH12 NARG 2 3.171 -4.817 -0.604 0.00 0.00<br>ATOM 61 HH22 NARG 2 4.299 -3.631 1.035 0.00 0.00<br>ATOM 62 H1 NARG 2 -5.466 -5.584 2.740 0.00 0.00<br>ATOM 63 H2 NARG 2 -4.525 -6.890 2.463 0.00 0.00<br>
ATOM 64 H3 NARG 2 -4.783 -5.802 1.272 0.00 0.00<br>END<br><br><br><br><div class="gmail_quote">On Wed, Nov 4, 2009 at 7:54 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">Chandan Choudhury wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi everyone !!<br>
<br>
I am having a problem using pdb2gmx command. Using the command on my input pdb file, it results saying Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms. I do not have only "O" either in input pdb file or in rtp file. and its O and not 0 (zero).<br>
<br>
My part of input files reads as <br>
ATOM 1 N CCMT 1 -2.521 -2.813 2.083 0.00 0.00<br>
ATOM 2 CA CCMT 1 -2.925 -1.739 1.166 0.00 0.00<br>
ATOM 3 C CCMT 1 -1.711 -0.842 0.859 0.00 0.00<br>
ATOM 4 CB CCMT 1 -4.034 -0.895 1.821 0.00 0.00<br>
ATOM 5 SG CCMT 1 -4.523 0.408 0.710 0.00 0.00<br>
ATOM 6 SD CCMT 1 -5.981 1.512 1.567 0.00 0.00<br>
ATOM 7 CE CCMT 1 -7.394 0.480 1.895 0.00 0.00<br>
ATOM 8 CZ CCMT 1 -6.988 -0.662 2.846 0.00 0.00<br>
ATOM 9 CH CCMT 1 -7.604 -2.072 2.895 0.00 0.00<br>
ATOM 10 CH1 CCMT 1 -8.797 -2.090 3.869 0.00 0.00<br>
ATOM 11 CH2 CCMT 1 -8.096 -2.574 1.525 0.00 0.00<br>
ATOM 12 CI CCMT 1 -5.986 -1.995 4.476 0.00 0.00<br>
ATOM 13 CI1 CCMT 1 -4.582 -2.406 4.958 0.00 0.00<br>
ATOM 14 CI2 CCMT 1 -6.931 -2.001 5.692 0.00 0.00<br>
ATOM 15 CK CCMT 1 -6.018 -0.615 3.792 0.00 0.00<br>
ATOM 16 NT1 CCMT 1 -6.486 -2.876 3.411 0.00 0.00<br>
ATOM 17 OC1 CCMT 1 -0.511 -1.346 0.867 0.00 0.00<br>
ATOM 18 OC2 CCMT 1 -1.885 0.420 0.592 0.00 0.00<br>
ATOM 19 OT1 CCMT 1 -6.836 -4.122 3.830 0.00 0.00<br>
ATOM 20 H CCMT 1 -1.801 -3.362 1.658 0.00 0.00<br>
ATOM 21 HA CCMT 1 -3.292 -2.165 0.256 0.00 0.00<br>
ATOM 22 HB1 CCMT 1 -4.878 -1.518 2.033 0.00 0.00<br>
ATOM 23 HB2 CCMT 1 -3.668 -0.468 2.731 0.00 0.00<br>
ATOM 24 HE1 CCMT 1 -7.754 0.067 0.976 0.00 0.00<br>
ATOM 25 HE2 CCMT 1 -8.165 1.065 2.350 0.00 0.00<br>
ATOM 26 HH11 CCMT 1 -9.175 -3.088 3.952 0.00 0.00<br>
ATOM 27 HH21 CCMT 1 -8.875 -1.932 1.170 0.00 0.00<br>
ATOM 28 HH12 CCMT 1 -8.477 -1.749 4.832 0.00 0.00<br>
ATOM 29 HH22 CCMT 1 -7.283 -2.566 0.829 0.00 0.00<br>
ATOM 30 HH13 CCMT 1 -9.567 -1.446 3.500 0.00 0.00<br>
ATOM 31 HH23 CCMT 1 -8.471 -3.571 1.624 0.00 0.00<br>
ATOM 32 HI11 CCMT 1 -4.241 -1.712 5.697 0.00 0.00<br>
ATOM 33 HI21 CCMT 1 -6.956 -2.982 6.119 0.00 0.00<br>
ATOM 34 HI12 CCMT 1 -4.624 -3.387 5.383 0.00 0.00<br>
ATOM 35 HI22 CCMT 1 -6.577 -1.303 6.422 0.00 0.00<br>
ATOM 36 HI13 CCMT 1 -3.906 -2.405 4.128 0.00 0.00<br>
ATOM 37 HI23 CCMT 1 -7.915 -1.722 5.380 0.00 0.00<br>
ATOM 38 HK CCMT 1 -5.391 0.221 4.019 0.00 0.00<br>
</blockquote>
<br></div></div>
What's next in the input PDB file?<br><font color="#888888">
<br>
Mark<br>
<br>
</font><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
and my part of .rtp file is<br>
[ CCMT ]<br>
[ atoms ]<br>
N amber99_34 -0.396165 1<br>
H amber99_17 0.295187 2<br>
CA amber99_11 -0.073501 3<br>
HA amber99_19 0.140510 4<br>
CB amber99_11 -0.221371 5<br>
HB1 amber99_19 0.146537 6<br>
HB2 amber99_19 0.146537 7<br>
SG amber99_48 -0.285182 8<br>
SD amber99_68 -0.08 9 ;SM<br>
CE amber99_69 -0.10 10<br>
HE1 amber99_70 -0.09 11<br>
HE2 amber99_70 -0.09 12<br>
CZ amber99_71 -0.003 13<br>
CH amber99_73 0.334 14<br>
CH1 amber99_74 -0.337 15<br>
HH11 amber99_76 0.090 16<br>
HH12 amber99_76 0.090 17<br>
HH13 amber99_76 0.090 18<br>
CH2 amber99_74 -0.337 19<br>
HH21 amber99_76 0.090 20<br>
HH22 amber99_76 0.090 21<br>
HH23 amber99_76 0.090 22<br>
NT1 amber99_77 0.220 23<br>
OT1 amber99_78 -0.438 24<br>
CI amber99_75 0.329 25<br>
CI1 amber99_74 -0.337 26<br>
HI11 amber99_76 0.090 27<br>
HI12 amber99_76 0.090 28<br>
HI13 amber99_76 0.090 29<br>
CI2 amber99_74 -0.337 30<br>
HI21 amber99_76 0.090 31<br>
HI22 amber99_76 0.090 32<br>
HI23 amber99_76 0.090 33<br>
CK amber99_72 -0.340 34<br>
HK amber99_79 0.162 35<br>
C amber99_2 0.643035 36<br>
OC1 amber99_45 -0.79810 37<br>
OC2 amber99_45 -0.79810 38<br>
<br>
Any help is heartly welcomed.<br>
Thanks in advance<br>
<br>
Chandan<br>
<br>
-- <br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br>
<br></div></div>
------------------------------------------------------------------------<div class="im"><br>
<br>
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</div></blockquote><div><div></div><div class="h5">
_______________________________________________<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>