Problem is solved. The atom needed to be called O not O2.<div><br class="webkit-block-placeholder"></div><div>Thanks,<br><br><div class="gmail_quote">On Tue, Sep 15, 2009 at 11:29 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Gunnar Widtfeldt Reginsson wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi. Can someone please help me.<br>
<br>
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:<br>
'Atom 02 in residue DT 3 not found in rtp entry with 32 atoms while sorting atoms'<br>
<br>
Here is the portion of the pdb file containing the atom in question:<br>
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 <br>
Where atom 02 must be O1P in DT 3<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
It could be a problem of formatting (incorrect spacing), or somewhere else in the residue you have an atom labeled 02 (with a zero).<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
Here is the portion of the amber99 .rtf file for the DT nucleotide:<br>
[ DT ]<br>
[ atoms ]<br>
P amber99_46 1.16590 1<br>
O1P amber99_45 -0.77610 2<br>
O2P amber99_45 -0.77610 3<br>
O5' amber99_44 -0.49540 4<br>
C5' amber99_11 -0.00690 5<br>
H5'1 amber99_19 0.07540 6<br>
H5'2 amber99_19 0.07540 7<br>
C4' amber99_11 0.16290 8<br>
H4' amber99_19 0.11760 9<br>
O4' amber99_44 -0.36910 10<br>
C1' amber99_11 0.06800 11<br>
H1' amber99_20 0.18040 12<br>
N1 amber99_40 -0.02390 13<br>
C6 amber99_7 -0.22090 14<br>
H6 amber99_23 0.26070 15<br>
C5 amber99_7 0.00250 16<br>
C7 amber99_11 -0.22690 17<br>
H71 amber99_18 0.07700 18<br>
H72 amber99_18 0.07700 19<br>
H73 amber99_18 0.07700 20<br>
C4 amber99_2 0.51940 21<br>
O4 amber99_41 -0.55630 22<br>
N3 amber99_35 -0.43400 23<br>
H3 amber99_17 0.34200 24<br>
C2 amber99_2 0.56770 25<br>
O amber99_41 -0.58810 26<br>
C3' amber99_11 0.07130 27<br>
H3' amber99_19 0.09850 28<br>
C2' amber99_11 -0.08540 29<br>
H2'1 amber99_18 0.07180 30<br>
H2'2 amber99_18 0.07180 31<br>
O3' amber99_44 -0.52320 32<br>
<br>
I can't see why atom 02 shouldn't be found.<br>
<br>
I am running GROMACS 4.0.5 on Mac OS 10.5<br>
<br>
Thanks,<br>
Gunnar W.<br>
<br>
<br></div></div>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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