<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">William Welch</b> <span dir="ltr"><<a href="mailto:wwelch000@gmail.com">wwelch000@gmail.com</a>></span><br>
Date: Wed, Sep 28, 2011 at 3:43 PM<br>Subject: pdb2gmx converting coordinates incorrectly.<br>To: <a href="mailto:gmxusers@gromacs.org">gmxusers@gromacs.org</a><br><br><br>Friends, <br>I generated a pdb for a tyrosineamide molecule and made an entry for it in ffcharmm27.rtp. Everything seems to be fucntional--I can make the .gro file and the .top file using pdb2gmx and subsequent processes seem to execute fine. The only problem is that when I look at the .gro file in VMD, I can see that the atoms have been moved to entirely different coordinates with respect to each other---I mean it's not even a real molecule, and certainly not the one I'm starting with Looking at the text of the .gro file, I see that the x cooridinate seems to have been converted correctly to nanometers, but the y and z coordinates are clearly wrong. Here are copies of the coordinates (the columns are aligned in the real files). This happens when I use pdb2gmx Version 4.0.5 <br>
<br><br>PDB <br>TITLE tyrosineamide2 <br>REMARK 4<br>REMARK 4 COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996<br>REMARK 6 created by ArgusLab version 4.0.1<br>REMARK 6 <a href="http://www.arguslab.com" target="_blank">http://www.arguslab.com</a><br>
REMARK 6<br>ATOM 1 NH3 TYRA ? 1 -1.797 5.686 -1.030 N<br>ATOM 2 CA TYRA ? 1 -1.575 4.269 -0.716 C<br>ATOM 3 C TYRA ? 1 -0.273 3.854 -1.311 C<br>
ATOM 4 O TYRA ? 1 0.570 3.201 -0.654 O<br>ATOM 5 CB TYRA ? 1 -2.734 3.441 -1.274 C<br>ATOM 6 CG TYRA ? 1 -3.924 3.374 -0.339 C<br>
ATOM 7 CD1 TYRA ? 1 -3.942 2.496 0.665 C<br>ATOM 8 CD2 TYRA ? 1 -5.007 4.235 -0.538 C<br>ATOM 9 CE1 TYRA ? 1 -5.072 2.449 1.563 C<br>
ATOM 10 CE2 TYRA ? 1 -6.152 4.156 0.320 C<br>ATOM 11 CZ TYRA ? 1 -6.140 3.253 1.299 C<br>ATOM 12 OH TYRA ? 1 -7.278 3.176 2.149 O<br>
ATOM 13 NH2 TYRA ? 1 0.019 4.207 -2.655 N<br>ATOM 14 HA TYRA ? 1 -1.536 4.134 0.375 H<br>ATOM 15 HB1 TYRA ? 1 -3.064 3.890 -2.223 H<br>
ATOM 16 HB2 TYRA ? 1 -2.380 2.416 -1.457 H<br>ATOM 17 HD1 TYRA ? 1 -3.096 1.808 0.810 H<br>ATOM 18 HD2 TYRA ? 1 -4.980 4.973 -1.354 H<br>
ATOM 19 HE1 TYRA ? 1 -5.055 1.776 2.433 H<br>ATOM 20 HE2 TYRA ? 1 -7.007 4.829 0.160 H<br>ATOM 21 HH TYRA ? 1 -7.154 2.339 2.852 H<br>
ATOM 22 HC1 TYRA ? 1 -0.899 6.265 -0.766 H<br>ATOM 23 HC2 TYRA ? 1 -2.656 6.059 -0.453 H<br>ATOM 24 HC3 TYRA ? 1 -2.000 5.796 -2.105 H<br>
ATOM 25 HN1 TYRA ? 1 0.976 3.907 -3.107 H<br>ATOM 26 HN2 TYRA ? 1 -0.682 3.761 -3.376 H<br><br>.gro<br> tyrosineamide2<br> 26<br> 1TYRA NH3 1 -0.179 0.700 0.600<br>
1TYRA HC1 2 -0.089 0.900 0.500<br> 1TYRA HC2 3 -0.265 0.600 0.900<br> 1TYRA HC3 4 -0.200 0.000 0.600<br> 1TYRA CA 5 -0.157 0.500 0.900<br> 1TYRA HA 6 -0.153 0.600 0.400<br>
1TYRA CB 7 -0.273 0.400 0.100<br> 1TYRA HB1 8 -0.306 0.400 0.000<br> 1TYRA HB2 9 -0.238 0.000 0.600<br> 1TYRA CG 10 -0.392 0.400 0.400<br> 1TYRA CD1 11 -0.394 0.200 0.600<br>
1TYRA HD1 12 -0.309 0.600 0.800<br> 1TYRA CE1 13 -0.507 0.200 0.900<br> 1TYRA HE1 14 -0.505 0.500 0.600<br> 1TYRA CZ 15 -0.614 0.000 0.300<br> 1TYRA OH 16 -0.727 0.800 0.600<br>
1TYRA HH 17 -0.715 0.400 0.900<br> 1TYRA CD2 18 -0.500 0.700 0.500<br> 1TYRA HD2 19 -0.498 0.000 0.300<br> 1TYRA CE2 20 -0.615 0.200 0.600<br> 1TYRA HE2 21 -0.700 0.700 0.900<br>
1TYRA C 22 -0.027 0.300 0.400<br> 1TYRA O 23 0.057 0.000 0.100<br> 1TYRA NH2 24 0.001 0.900 0.700<br> 1TYRA HN1 25 0.097 0.600 0.700<br> 1TYRA HN2 26 -0.068 0.200 0.100<br>
0.82400 0.90000 0.90000<br><br>Will<br>
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