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