Gunnar Widtfeldt Reginsson wrote:
Hi. Can someone please help me.
I am new to Gromacs. I have a 20mer DNA duplex I want to do some MD on.
I start by making a topology file form the pdb file. When I run pdb2gmx
and the amber99 force field I get this fatal error:
'Atom 02 in residue DT 3 not found in rtp entry with 32 atoms while
sorting atoms'
Here is the portion of the pdb file containing the atom in question:
ATOM 37 C4 DA A 2 2.705 -1.868 3.118 1.00 0.00
ATOM 38 C3' DA A 2 6.858 -4.420 2.715 1.00 0.00
ATOM 39 C2' DA A 2 5.664 -4.141 3.627 1.00 0.00
ATOM 40 O3' DA A 2 7.933 -3.562 3.073 1.00 0.00
ATOM 41 P DT A 3 8.308 -3.390 4.619 1.00 0.00
ATOM 42 O1P DT A 3 9.773 -3.228 4.760 1.00 0.00
ATOM 43 O2P DT A 3 7.705 -4.493 5.401 1.00 0.00
ATOM 44 O5' DT A 3 7.575 -2.013 4.972 1.00 0.00
ATOM 45 C5' DT A 3 7.588 -0.948 4.004 1.00 0.00
Where atom 02 must be O1P in DT 3
I don't know how you reach the conclusion that pdb2gmx is confusing atom 02
(which by the way is a "zero"-2 in the error message, not an "oh", if you have
copied and pasted directly) with atom O1P.
It could be a problem of formatting (incorrect spacing), or somewhere else in
the residue you have an atom labeled 02 (with a zero).
-Justin
Here is the portion of the amber99 .rtf file for the DT nucleotide:
[ DT ]
[ atoms ]
P amber99_46 1.16590 1
O1P amber99_45 -0.77610 2
O2P amber99_45 -0.77610 3
O5' amber99_44 -0.49540 4
C5' amber99_11 -0.00690 5
H5'1 amber99_19 0.07540 6
H5'2 amber99_19 0.07540 7
C4' amber99_11 0.16290 8
H4' amber99_19 0.11760 9
O4' amber99_44 -0.36910 10
C1' amber99_11 0.06800 11
H1' amber99_20 0.18040 12
N1 amber99_40 -0.02390 13
C6 amber99_7 -0.22090 14
H6 amber99_23 0.26070 15
C5 amber99_7 0.00250 16
C7 amber99_11 -0.22690 17
H71 amber99_18 0.07700 18
H72 amber99_18 0.07700 19
H73 amber99_18 0.07700 20
C4 amber99_2 0.51940 21
O4 amber99_41 -0.55630 22
N3 amber99_35 -0.43400 23
H3 amber99_17 0.34200 24
C2 amber99_2 0.56770 25
O amber99_41 -0.58810 26
C3' amber99_11 0.07130 27
H3' amber99_19 0.09850 28
C2' amber99_11 -0.08540 29
H2'1 amber99_18 0.07180 30
H2'2 amber99_18 0.07180 31
O3' amber99_44 -0.52320 32
I can't see why atom 02 shouldn't be found.
I am running GROMACS 4.0.5 on Mac OS 10.5
Thanks,
Gunnar W.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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