Hi to all<br><br><br>Sorry Justin , I try to correct spacing but now it stuck to another problem <br><br>pdb to TFE is as follow <br><br>OMPND UNNAMED<br>AUTHOR GENERATED BY OPEN BABEL 2.3.0<br>ATOM 1 CT TFE 1 -5.510 2.534 0.093 1.00 0.00 C <br>
ATOM 2 CH2T TFE 1 -6.061 1.111 0.155 1.00 0.00 C <br>ATOM 3 F1T TFE 1 -5.017 2.899 1.300 1.00 0.00 F <br>ATOM 4 F2T TFE 1 -6.461 3.426 -0.251 1.00 0.00 F <br>
ATOM 5 F3T TFE 1 -4.506 2.627 -0.806 1.00 0.00 F <br>ATOM 6 OT TFE 1 -7.065 0.921 1.164 1.00 0.00 O <br>ATOM 7 H TFE 1 -5.248 0.409 0.367 1.00 0.00 H <br>
ATOM 8 H TFE 1 -6.500 0.837 -0.808 1.00 0.00 H <br>ATOM 9 HT TFE 1 -6.742 1.339 1.982 1.00 0.00 H <br>CONECT 1 2 3 4 5 <br>
CONECT 1 <br>CONECT 2 1 6 7 8 <br>CONECT 2 <br>
CONECT 3 1 <br>CONECT 4 1 <br>CONECT 5 1 <br>
CONECT 6 2 9 <br>CONECT 7 2 <br>CONECT 8 2 <br>
CONECT 9 6 <br>MASTER 0 0 0 0 0 0 0 0 9 0 9 0<br>END<br><br><br>after giving pdb2gmx -ignh <br><br>It give following error <br>
WARNING: atom HT is missing in residue TFE 1 in the pdb file<br> You might need to add atom HT to the hydrogen database of building block TFE<br> in the file aminoacids.hdb (see the manual)<br><br><br>-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.5.4<br>Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1463<br><br>Fatal error:<br>There were 1 missing atoms in molecule Other, if you want to use this incomplete topology anyhow, use the option -missing<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------<br>
<br>-------------------------------------------------------<br> now I know go with missing is wrong ..But to check error I goes with -missing flag .<br>the output confo.gro is as follow <br><br>UNNAMED<br> 6<br> 1TFE OT 1 -0.706 0.092 0.116<br>
1TFE CH2T 2 -0.606 0.111 0.015<br> 1TFE CT 3 -0.551 0.253 0.009<br> 1TFE F1T 4 -0.502 0.290 0.130<br> 1TFE F2T 5 -0.646 0.343 -0.025<br> 1TFE F3T 6 -0.451 0.263 -0.081<br>
0.25590 0.25050 0.21060<br><br>The hydrogen attched to oxyge is missing ..<br>The entry to these hydrogen as HT is mentioned in pdb file ...<br><br>The warning message is self-explanatory.<br>I will be a very greatfull to you if you told me how to add HT <br>
in aminoacids.hdb<br>Aminoacids.hdb file is as follow ....<br> <br>SER 2 <br>1 1 H N -C CA<br>1 2 HG OG CB CA<br><b>TFE 1 <br>1 2 H O CH2 C</b><br>THR 2 <br>
1 1 H N -C CA<br>1 2 HG1 OG1 CB CA<br>TRP 7 <br>1 1 H N -C CA<br>1 1 HD1 CD1 CG NE1<br><br>So What line I have to add here???<br><br>Please suggest me the way out to get rid from error ..<br>
<br><br>Rama David <br><br>