Chandan Choudhury wrote:
My complete input file is
ATOM 1 N CCMT 1 -2.521 -2.813 2.083 0.00 0.00
ATOM 2 CA CCMT 1 -2.925 -1.739 1.166 0.00 0.00
ATOM 3 C CCMT 1 -1.711 -0.842 0.859 0.00 0.00
ATOM 4 CB CCMT 1 -4.034 -0.895 1.821 0.00 0.00
ATOM 5 SG CCMT 1 -4.523 0.408 0.710 0.00 0.00
ATOM 6 SD CCMT 1 -5.981 1.512 1.567 0.00 0.00
ATOM 7 CE CCMT 1 -7.394 0.480 1.895 0.00 0.00
ATOM 8 CZ CCMT 1 -6.988 -0.662 2.846 0.00 0.00
ATOM 9 CH CCMT 1 -7.604 -2.072 2.895 0.00 0.00
ATOM 10 CH1 CCMT 1 -8.797 -2.090 3.869 0.00 0.00
ATOM 11 CH2 CCMT 1 -8.096 -2.574 1.525 0.00 0.00
ATOM 12 CI CCMT 1 -5.986 -1.995 4.476 0.00 0.00
ATOM 13 CI1 CCMT 1 -4.582 -2.406 4.958 0.00 0.00
ATOM 14 CI2 CCMT 1 -6.931 -2.001 5.692 0.00 0.00
ATOM 15 CK CCMT 1 -6.018 -0.615 3.792 0.00 0.00
ATOM 16 NT1 CCMT 1 -6.486 -2.876 3.411 0.00 0.00
ATOM 17 OC1 CCMT 1 -0.511 -1.346 0.867 0.00 0.00
ATOM 18 OC2 CCMT 1 -1.885 0.420 0.592 0.00 0.00
ATOM 19 OT1 CCMT 1 -6.836 -4.122 3.830 0.00 0.00
ATOM 20 H CCMT 1 -1.801 -3.362 1.658 0.00 0.00
ATOM 21 HA CCMT 1 -3.292 -2.165 0.256 0.00 0.00
ATOM 22 HB1 CCMT 1 -4.878 -1.518 2.033 0.00 0.00
ATOM 23 HB2 CCMT 1 -3.668 -0.468 2.731 0.00 0.00
ATOM 24 HE1 CCMT 1 -7.754 0.067 0.976 0.00 0.00
ATOM 25 HE2 CCMT 1 -8.165 1.065 2.350 0.00 0.00
ATOM 26 HH11 CCMT 1 -9.175 -3.088 3.952 0.00 0.00
ATOM 27 HH21 CCMT 1 -8.875 -1.932 1.170 0.00 0.00
ATOM 28 HH12 CCMT 1 -8.477 -1.749 4.832 0.00 0.00
ATOM 29 HH22 CCMT 1 -7.283 -2.566 0.829 0.00 0.00
ATOM 30 HH13 CCMT 1 -9.567 -1.446 3.500 0.00 0.00
ATOM 31 HH23 CCMT 1 -8.471 -3.571 1.624 0.00 0.00
ATOM 32 HI11 CCMT 1 -4.241 -1.712 5.697 0.00 0.00
ATOM 33 HI21 CCMT 1 -6.956 -2.982 6.119 0.00 0.00
ATOM 34 HI12 CCMT 1 -4.624 -3.387 5.383 0.00 0.00
ATOM 35 HI22 CCMT 1 -6.577 -1.303 6.422 0.00 0.00
ATOM 36 HI13 CCMT 1 -3.906 -2.405 4.128 0.00 0.00
ATOM 37 HI23 CCMT 1 -7.915 -1.722 5.380 0.00 0.00
ATOM 38 HK CCMT 1 -5.391 0.221 4.019 0.00 0.00
ATOM 39 N NARG 2 -4.657 -5.920 2.257 0.00 0.00
ATOM 40 CA NARG 2 -3.476 -5.161 2.694 0.00 0.00
ATOM 41 C NARG 2 -3.680 -3.668 2.378 0.00 0.00
ATOM 42 O NARG 2 -4.839 -3.179 2.371 0.00 0.00
ATOM 43 CB NARG 2 -2.230 -5.679 1.952 0.00 0.00
ATOM 44 CG NARG 2 -0.992 -4.885 2.410 0.00 0.00
ATOM 45 CZ NARG 2 2.459 -4.459 1.265 0.00 0.00
ATOM 46 CD NARG 2 0.254 -5.404 1.668 0.00 0.00
ATOM 47 NE NARG 2 1.436 -4.648 2.106 0.00 0.00
ATOM 48 NH1 NARG 2 2.406 -4.958 0.025 0.00 0.00
ATOM 49 NH2 NARG 2 3.535 -3.771 1.664 0.00 0.00
ATOM 50 HA NARG 2 -3.341 -5.287 3.748 0.00 0.00
ATOM 51 HB1 NARG 2 -2.089 -6.716 2.172 0.00 0.00
ATOM 52 HB2 NARG 2 -2.365 -5.552 0.898 0.00 0.00
ATOM 53 HG1 NARG 2 -1.132 -3.847 2.190 0.00 0.00
ATOM 54 HG2 NARG 2 -0.858 -5.011 3.464 0.00 0.00
ATOM 55 HD1 NARG 2 0.393 -6.442 1.888 0.00 0.00
ATOM 56 HD2 NARG 2 0.120 -5.278 0.614 0.00 0.00
ATOM 57 HE NARG 2 1.475 -4.274 3.033 0.00 0.00
ATOM 58 HH11 NARG 2 1.602 -5.472 -0.274 0.00 0.00
ATOM 59 HH21 NARG 2 3.574 -3.398 2.591 0.00 0.00
ATOM 60 HH12 NARG 2 3.171 -4.817 -0.604 0.00 0.00
ATOM 61 HH22 NARG 2 4.299 -3.631 1.035 0.00 0.00
ATOM 62 H1 NARG 2 -5.466 -5.584 2.740 0.00 0.00
ATOM 63 H2 NARG 2 -4.525 -6.890 2.463 0.00 0.00
ATOM 64 H3 NARG 2 -4.783 -5.802 1.272 0.00 0.00
END
This looks like you are trying to convert a non-covalently-bound ligand
and an ARG-terminated protein in the same structure. If you'd described
what you were trying to do in words in your first post, that would have
been helpful. Your approach might work if you use PDB chain identifiers
properly.
Also possible is to run pdb2gmx on isolated ligand, and separately on
isolated protein. Edit the two top files to convert them to .itp files,
and #include them in a new master .top file. This might be a good idea
for some workflows. See
http://www.gromacs.org/Documentation/File_Formats/.top_File and links
from it.
Mark
On Wed, Nov 4, 2009 at 7:54 AM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
Chandan Choudhury wrote:
Hi everyone !!
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).
My part of input files reads as
ATOM 1 N CCMT 1 -2.521 -2.813 2.083 0.00 0.00
ATOM 2 CA CCMT 1 -2.925 -1.739 1.166 0.00 0.00
ATOM 3 C CCMT 1 -1.711 -0.842 0.859 0.00 0.00
ATOM 4 CB CCMT 1 -4.034 -0.895 1.821 0.00 0.00
ATOM 5 SG CCMT 1 -4.523 0.408 0.710 0.00 0.00
ATOM 6 SD CCMT 1 -5.981 1.512 1.567 0.00 0.00
ATOM 7 CE CCMT 1 -7.394 0.480 1.895 0.00 0.00
ATOM 8 CZ CCMT 1 -6.988 -0.662 2.846 0.00 0.00
ATOM 9 CH CCMT 1 -7.604 -2.072 2.895 0.00 0.00
ATOM 10 CH1 CCMT 1 -8.797 -2.090 3.869 0.00 0.00
ATOM 11 CH2 CCMT 1 -8.096 -2.574 1.525 0.00 0.00
ATOM 12 CI CCMT 1 -5.986 -1.995 4.476 0.00 0.00
ATOM 13 CI1 CCMT 1 -4.582 -2.406 4.958 0.00 0.00
ATOM 14 CI2 CCMT 1 -6.931 -2.001 5.692 0.00 0.00
ATOM 15 CK CCMT 1 -6.018 -0.615 3.792 0.00 0.00
ATOM 16 NT1 CCMT 1 -6.486 -2.876 3.411 0.00 0.00
ATOM 17 OC1 CCMT 1 -0.511 -1.346 0.867 0.00 0.00
ATOM 18 OC2 CCMT 1 -1.885 0.420 0.592 0.00 0.00
ATOM 19 OT1 CCMT 1 -6.836 -4.122 3.830 0.00 0.00
ATOM 20 H CCMT 1 -1.801 -3.362 1.658 0.00 0.00
ATOM 21 HA CCMT 1 -3.292 -2.165 0.256 0.00 0.00
ATOM 22 HB1 CCMT 1 -4.878 -1.518 2.033 0.00 0.00
ATOM 23 HB2 CCMT 1 -3.668 -0.468 2.731 0.00 0.00
ATOM 24 HE1 CCMT 1 -7.754 0.067 0.976 0.00 0.00
ATOM 25 HE2 CCMT 1 -8.165 1.065 2.350 0.00 0.00
ATOM 26 HH11 CCMT 1 -9.175 -3.088 3.952 0.00 0.00
ATOM 27 HH21 CCMT 1 -8.875 -1.932 1.170 0.00 0.00
ATOM 28 HH12 CCMT 1 -8.477 -1.749 4.832 0.00 0.00
ATOM 29 HH22 CCMT 1 -7.283 -2.566 0.829 0.00 0.00
ATOM 30 HH13 CCMT 1 -9.567 -1.446 3.500 0.00 0.00
ATOM 31 HH23 CCMT 1 -8.471 -3.571 1.624 0.00 0.00
ATOM 32 HI11 CCMT 1 -4.241 -1.712 5.697 0.00 0.00
ATOM 33 HI21 CCMT 1 -6.956 -2.982 6.119 0.00 0.00
ATOM 34 HI12 CCMT 1 -4.624 -3.387 5.383 0.00 0.00
ATOM 35 HI22 CCMT 1 -6.577 -1.303 6.422 0.00 0.00
ATOM 36 HI13 CCMT 1 -3.906 -2.405 4.128 0.00 0.00
ATOM 37 HI23 CCMT 1 -7.915 -1.722 5.380 0.00 0.00
ATOM 38 HK CCMT 1 -5.391 0.221 4.019 0.00 0.00
What's next in the input PDB file?
Mark
and my part of .rtp file is
[ CCMT ]
[ atoms ]
N amber99_34 -0.396165 1
H amber99_17 0.295187 2
CA amber99_11 -0.073501 3
HA amber99_19 0.140510 4
CB amber99_11 -0.221371 5
HB1 amber99_19 0.146537 6
HB2 amber99_19 0.146537 7
SG amber99_48 -0.285182 8
SD amber99_68 -0.08 9 ;SM
CE amber99_69 -0.10 10
HE1 amber99_70 -0.09 11
HE2 amber99_70 -0.09 12
CZ amber99_71 -0.003 13
CH amber99_73 0.334 14
CH1 amber99_74 -0.337 15
HH11 amber99_76 0.090 16
HH12 amber99_76 0.090 17
HH13 amber99_76 0.090 18
CH2 amber99_74 -0.337 19
HH21 amber99_76 0.090 20
HH22 amber99_76 0.090 21
HH23 amber99_76 0.090 22
NT1 amber99_77 0.220 23
OT1 amber99_78 -0.438 24
CI amber99_75 0.329 25
CI1 amber99_74 -0.337 26
HI11 amber99_76 0.090 27
HI12 amber99_76 0.090 28
HI13 amber99_76 0.090 29
CI2 amber99_74 -0.337 30
HI21 amber99_76 0.090 31
HI22 amber99_76 0.090 32
HI23 amber99_76 0.090 33
CK amber99_72 -0.340 34
HK amber99_79 0.162 35
C amber99_2 0.643035 36
OC1 amber99_45 -0.79810 37
OC2 amber99_45 -0.79810 38
Any help is heartly welcomed.
Thanks in advance
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
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--
Chandan kumar Choudhury
NCL, Pune
INDIA
------------------------------------------------------------------------
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