On 5/15/12 9:54 AM, rama david wrote:
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
The spacing in this file is still potentially problematic.
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
If you delete the two extraneous H atoms in the .pdb file and omit -ignh, you
won't have this problem.
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*
The corrected line would read:
1 2 HT OT CH2T CT
This is a small bug that should probably be fixed, though in your case, with
proper input, use of the .hdb file is unnecessary.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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