[gmx-users] about trifloroehanol

[Justin A. Lemkul]

On 5/15/12 8:25 AM, rama david wrote:
>   Hi all
>
>   Very sorry for my stupid question .. I really work a lot on these problem
>
> I wish to use Trifluroethanol  as solvent  for
> my study ...
>
> I Check the top file for G96 53a6 ff
>
> It shows TFE with following lines ...
>
>
> [ TFE ]
>   [ atoms ]
>     HT     H     0.41000     0
>     OT  OTFE    -0.62500     0
>   CH2T CHTFE     0.27300     0
>     CT  CTFE     0.45200     0
>    F1T  FTFE    -0.17000     0
>    F2T  FTFE    -0.17000     0
>    F3T  FTFE    -0.17000     0
>   [ bonds ]
>     HT    OT    gb_1
>     OT  CH2T    gb_18
>   CH2T    CT    gb_27
>     CT   F1T    gb_13
>     CT   F2T    gb_13
>     CT   F3T    gb_13
>   [ angles ]
> ;  ai    aj    ak   gromos type
>     HT    OT  CH2T     ga_50
>     OT  CH2T    CT     ga_51
>   CH2T    CT   F1T     ga_52
>   CH2T    CT   F2T     ga_52
>   CH2T    CT   F3T     ga_52
>    F1T    CT   F2T     ga_49
>    F1T    CT   F3T     ga_49
>    F2T    CT   F3T     ga_49
>   [ impropers ]
> ;  ai    aj    ak    al   gromos type
>   [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>     HT    OT  CH2T    CT     gd_24
>
>
> I draw  TFE with Avogadro software...
>
> I get following pdb  ..
>
> COMPND    UNNAMED
> AUTHOR    GENERATED BY OPEN BABEL 2.3.0
> HETATM    1  C   LIG     1      -7.301   3.857   0.070  1.00  0.00           C
> HETATM    2  C   LIG     1      -6.798   2.416   0.102  1.00  0.00           C
> HETATM    3  F   LIG     1      -8.626   3.915   0.327  1.00  0.00           F
> HETATM    4  F   LIG     1      -7.094   4.399  -1.153  1.00  0.00           F
> HETATM    5  F   LIG     1      -6.668   4.631   0.977  1.00  0.00           F
> HETATM    6  O   LIG     1      -5.426   2.272  -0.294  1.00  0.00           O
> HETATM    7  H   LIG     1      -7.399   1.800  -0.574  1.00  0.00           H
> HETATM    8  H   LIG     1      -6.898   2.006   1.111  1.00  0.00           H
> HETATM    9  H   LIG     1      -5.299   2.795  -1.107  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
>
>
> I change pdb as follow to match the nomenclature with G96 53a6 ff
> (Is it right or wrong ????)
>
> OMPND    UNNAMED
> AUTHOR    GENERATED BY OPEN BABEL 2.3.0
> HETATM    1   CT   TFE     1      -7.301   3.857   0.070  1.00  0.00           C
> HETATM    2 CH2T   TFE     1      -6.798   2.416   0.102  1.00  0.00           C
> HETATM    3  F1T   TFE     1      -8.626   3.915   0.327  1.00  0.00           F
> HETATM    4  F2T   TFE     1      -7.094   4.399  -1.153  1.00  0.00           F
> HETATM    5  F3T   TFE     1      -6.668   4.631   0.977  1.00  0.00           F
> HETATM    6   OT   TFE     1      -5.426   2.272  -0.294  1.00  0.00           O
> HETATM    7    H   TFE     1      -7.399   1.800  -0.574  1.00  0.00           H
> HETATM    8    H   TFE     1      -6.898   2.006   1.111  1.00  0.00           H
> HETATM    9   HT   TFE     1      -5.299   2.795  -1.107  1.00  0.00           H
> CONECT    1    2    3    4    5
>
> AFTER running pdb2gmx -ignh
>
>   I got following error ....
>
> ------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line: 581
>
> Fatal error:
> Residue 'F' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> I tried a lot ...
> Please give me some suggestion ...
> Thank you in Advance ...
>

The column spacing of a .pdb file is fixed and you must adhere to it.  The 
changes you have made look fine, but they are spaced incorrectly, thus pdb2gmx 
is not able to correctly read its contents.

-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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