ABEL Stephane 175950 wrote:
You are right Justin,
The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why
this problem happens ? Should I change the name of these atoms in the rtp and
pdb files ? Is a trick is available to avoid this "bad" translation ?
The only option is to not use digits as the first characters in an atom name.
The code in pdb2gmx.c calls a function "rename_atoms" in xlate.c, which (since a
value of TRUE is passed to the function for bReorderNum), shifts the position of
all digits in the first position:
if (bReorderNum)
{
if (isdigit(atombuf[0]))
{
c = atombuf[0];
for (i=0; ((size_t)i<strlen(atombuf)-1); i++)
{
atombuf[i] = atombuf[i+1];
}
atombuf[i] = c;
bReorderedNum = TRUE;
}
}
I think the purpose is really to deal with hydrogens (i.e. 1HG1, etc) but
affects all atoms, as written. A check could probably be implemented to
determine if the atom is H or not, but really might not be worth the effort,
since the vast majority of all structures that will be passed to pdb2gmx will
follow the normal route of: character first, then digits.
-Justin
Stefane
ABEL Stephane 175950 wrote:
Dear all,
I have a very "common" problem when I try to convert a pdb file to a gro
file with the following command.
I use charmm27ff and gmx4.5.1.
pdb2gmx_mpi -f 1-bDM.pdb -o 1-bDM.gro -p 1-bDM.top -chargegrp
I obtain the following "commun" error :
"Atom O11 in residue bDM 1 was not found in rtp entry bDM with 80 atoms
while sorting atoms".
I am surprised to have this message, since after verification in the
1-bDM.pdb, I have not found an atom with this name. I have also checked the
format of the pdb and all the fields are in right place.
Probably atom 1O1 is being translated as O11. I have had similar problems
with translated atom names. If you add "-debug 1" to your pdb2gmx command
line, you will get output .pdb files containing the structure as pdb2gmx is
interpreting it. That's how I've identified some spurious translations
before.
-Justin
Below my PDB file ATOM 1 1C1 bDM 1 -28.807 -8.973 -4.361
0.30 0.00 ATOM 2 H1A bDM 1 -28.976 -9.551 -3.427 0.10
0.00 ATOM 3 1O1 bDM 1 -27.541 -9.232 -4.796 -0.40 0.00
ATOM 4 1C2 bDM 1 -29.836 -9.352 -5.325 0.14 0.00 ATOM
5 H2A bDM 1 -30.783 -9.324 -4.746 0.09 0.00 ATOM 6 1O2
bDM 1 -29.680 -10.694 -5.733 -0.66 0.00 ATOM 7 H2OA bDM
1 -28.731 -10.800 -5.827 0.43 0.00 ATOM 8 1C3 bDM 1
-29.990 -8.385 -6.493 0.14 0.00 ATOM 9 H3A bDM 1 -29.086
-8.411 -7.139 0.09 0.00 ATOM 10 1O3 bDM 1 -31.239 -8.585
-7.237 -0.66 0.00 ATOM 11 H3OA bDM 1 -31.193 -8.053 -8.035
0.43 0.00 ATOM 12 1C4 bDM 1 -29.957 -6.922 -6.018 0.14
0.00 ATOM 13 H4A bDM 1 -30.923 -6.772 -5.490 0.09 0.00
ATOM 14 1O4 bDM 1 -29.963 -6.003 -7.122 -0.66 0.00 ATOM
15 H4OA bDM 1 -29.993 -5.118 -6.751 0.43 0.00 ATOM 16 1C5
bDM 1 -28.865 -6.650 -5.081 0.10 0.00 ATOM 17 H5A bDM
1 -27.963 -7.009 -5.622 0.10 0.00 ATOM 18 1C6 bDM 1
-28.730 -5.254 -4.552 0.05 0.00 ATOM 19 H61A bDM 1 -29.694
-5.009 -4.056 0.09 0.00 ATOM 20 H61B bDM 1 -28.509 -4.622
-5.438 0.09 0.00 ATOM 21 1O6 bDM 1 -27.593 -5.254 -3.684
-0.66 0.00 ATOM 22 H6OA bDM 1 -27.699 -5.900 -2.982 0.43
0.00 ATOM 23 1O5 bDM 1 -28.979 -7.582 -3.963 -0.40 0.00
ATOM 24 2C1 bDM 1 -23.620 -9.286 -3.000 0.20 0.00 ATOM
25 H1B bDM 1 -23.440 -10.274 -3.475 0.09 0.00 ATOM 26 2C2
bDM 1 -24.806 -9.283 -2.026 0.14 0.00 ATOM 27 H2B bDM
1 -24.867 -8.235 -1.662 0.09 0.00 ATOM 28 2O2 bDM 1
-24.477 -10.097 -0.884 -0.66 0.00 ATOM 29 H2OB bDM 1 -23.792
-9.775 -0.294 0.43 0.00 ATOM 30 2C3 bDM 1 -26.163 -9.642
-2.661 0.14 0.00 ATOM 31 H3B bDM 1 -26.142 -10.663 -3.098
0.09 0.00 ATOM 32 2O3 bDM 1 -27.232 -9.397 -1.722 -0.66
0.00 ATOM 33 H3OB bDM 1 -27.384 -10.156 -1.155 0.43 0.00
ATOM 34 2C4 bDM 1 -26.364 -8.872 -3.987 0.10 0.00 ATOM
35 H4B bDM 1 -26.533 -7.835 -3.626 0.10 0.00 ATOM 36 2C5
bDM 1 -25.089 -8.936 -4.892 0.25 0.00 ATOM 37 H5B bDM
1 -24.906 -9.942 -5.326 0.09 0.00 ATOM 38 2C6 bDM 1
-25.225 -7.980 -6.074 0.05 0.00 ATOM 39 H62A bDM 1 -25.159
-6.910 -5.780 0.09 0.00 ATOM 40 H62B bDM 1 -26.236 -8.045
-6.532 0.09 0.00 ATOM 41 2O5 bDM 1 -24.218 -8.289 -7.105
-0.66 0.00 ATOM 42 H5OB bDM 1 -24.661 -8.895 -7.704 0.43
0.00 ATOM 43 2O4 bDM 1 -24.011 -8.432 -4.077 -0.40 0.00
ATOM 44 2O1 bDM 1 -22.364 -8.895 -2.386 -0.30 0.00 ATOM
45 C7 bDM 1 -21.159 -9.105 -3.148 -0.11 0.00 ATOM 46 H7A
bDM 1 -20.922 -10.188 -3.228 0.09 0.00 ATOM 47 H7B bDM
1 -21.320 -8.848 -4.217 0.09 0.00 ATOM 48 C8 bDM 1
-19.961 -8.389 -2.410 -0.18 0.00 ATOM 49 H8A bDM 1 -19.829
-8.778 -1.378 0.09 0.00 ATOM 50 H8B bDM 1 -20.171 -7.300
-2.464 0.09 0.00 ATOM 51 C9 bDM 1 -18.547 -8.641 -3.005
-0.18 0.00 ATOM 52 H9A bDM 1 -18.718 -8.465 -4.089 0.09
0.00 ATOM 53 H9B bDM 1 -18.415 -9.744 -3.010 0.09 0.00
ATOM 54 C10 bDM 1 -17.452 -7.785 -2.397 -0.18 0.00 ATOM
55 H10A bDM 1 -16.675 -7.915 -3.180 0.09 0.00 ATOM 56 H10B
bDM 1 -17.700 -6.702 -2.407 0.09 0.00 ATOM 57 C11 bDM
1 -16.987 -8.238 -1.043 -0.18 0.00 ATOM 58 H11A bDM 1
-16.658 -9.299 -1.039 0.09 0.00 ATOM 59 H11B bDM 1 -17.874
-8.295 -0.376 0.09 0.00 ATOM 60 C12 bDM 1 -15.798 -7.399
-0.595 -0.18 0.00 ATOM 61 H12A bDM 1 -16.131 -6.343 -0.678
0.09 0.00 ATOM 62 H12B bDM 1 -14.966 -7.559 -1.314 0.09
0.00 ATOM 63 C13 bDM 1 -15.271 -7.639 0.808 -0.18 0.00
ATOM 64 H13A bDM 1 -15.139 -8.740 0.874 0.09 0.00 ATOM
65 H13B bDM 1 -15.946 -7.348 1.641 0.09 0.00 ATOM 66 C14
bDM 1 -13.783 -7.068 1.047 -0.18 0.00 ATOM 67 H14A bDM
1 -13.635 -7.658 1.976 0.09 0.00 ATOM 68 H14B bDM 1
-13.020 -7.442 0.331 0.09 0.00 ATOM 69 C15 bDM 1 -13.644
-5.563 1.231 -0.18 0.00 ATOM 70 H15A bDM 1 -14.224 -5.173
2.096 0.09 0.00 ATOM 71 H15B bDM 1 -14.037 -5.111 0.296
0.09 0.00 ATOM 72 C16 bDM 1 -12.181 -5.162 1.586 -0.18
0.00 ATOM 73 H16A bDM 1 -12.171 -4.210 2.159 0.09 0.00
ATOM 74 H16B bDM 1 -11.783 -5.869 2.345 0.09 0.00 ATOM
75 C17 bDM 1 -11.148 -4.862 0.380 -0.18 0.00 ATOM 76 H17A
bDM 1 -10.974 -5.725 -0.298 0.09 0.00 ATOM 77 H17B bDM
1 -11.602 -4.094 -0.283 0.09 0.00 ATOM 78 C18 bDM 1
-9.916 -4.271 0.993 -0.27 0.00 ATOM 79 H18A bDM 1 -10.161
-3.350 1.564 0.09 0.00 ATOM 80 H18B bDM 1 -9.245 -3.989
0.153 0.09 0.00 ATOM 81 H18C bDM 1 -9.391 -4.974 1.675
0.09 0.00 Any help will be appreciated ! Stefane
-- ========================================
Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu |
(540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
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End of gmx-users Digest, Vol 77, Issue 159
******************************************
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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