[gmx-users] about trifloroehanol

[Justin A. Lemkul]

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

-- 
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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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