Thank you, Justin!<br><br>I changed the output files to .gro. <br><br>pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.gro -water spce >& pdb2gmx.log<br># add water<br>editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log<br>
genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >& genbox.log<br><br>However, the overflow error still occurs in the gro file:<br><br>32448SOL HW299996 9.410 8.282 1.575<br>32449SOL OW99997 9.923 8.813 0.726<br>
32449SOL HW199998 9.874 8.726 0.735<br>32449SOL HW299999 9.900 8.856 0.639<br>32450SOL OW 0 0.018 7.452 0.502<br>32450SOL HW1 1 0.058 7.543 0.493<br>32450SOL HW2 2 -0.082 7.460 0.508<br>
32451SOL OW 3 9.507 8.424 1.264<br>32451SOL HW1 4 9.596 8.379 1.250<br><br>What's wrong? Thanks a lot!<br><br>Peggy<br><br><div class="gmail_quote">On Sat, Feb 14, 2009 at 2:40 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="Wj3C7c"><br>
<br>
Peggy Yao wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear all,<br>
<br>
Has anyone encountered the problem of atom index overflow in PDB files after adding water molecules?<br>
<br>
The following are what I did:<br>
<br>
pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.pdb -water spce >& pdb2gmx.log<br>
# add water<br>
editconf -bt cubic -f 1eia.pdb -o 1eia.pdb -c -d 0.9 >& editconf.log<br>
genbox -cp 1eia.pdb -cs spc216.gro -o 1eia_water.pdb -p 1eia.top >& genbox.log<br>
<br>
However, in 1eia_water.pdb, the atom index of the water section overflowed:<br>
<br>
ATOM 99996 HW2 SOL 2448 98.583 52.132 64.542 1.00 0.00<br>
ATOM 99997 OW SOL 2449 1.182 45.201 68.242 1.00 0.00<br>
ATOM 99998 HW1 SOL 2449 1.592 44.881 69.102 1.00 0.00<br>
ATOM 99999 HW2 SOL 2449 0.222 44.931 68.212 1.00 0.00<br>
ATOM 0 OW SOL 2450 93.503 42.681 67.002 1.00 0.00<br>
ATOM 1 HW1 SOL 2450 94.353 42.351 66.592 1.00 0.00<br>
ATOM 2 HW2 SOL 2450 93.633 42.831 67.982 1.00 0.00<br>
ATOM 3 OW SOL 2451 94.993 42.441 73.082 1.00 0.00<br>
<br>
How to solve this problem?<br>
<br>
</blockquote>
<br></div></div>
Well, the .pdb file format can only handle a fixed amount of digits when numbering atoms. I don't know if using .gro format will be of any use, but I routinely simulate systems of 200,000+ atoms with no problem, and any index files I make are correctly numbered.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks,<br>
Peggy<br>
<br>
<br>
------------------------------------------------------------------------<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<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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