[gmx-users] about trifloroehanol

[rama david]

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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