[gmx-users] about trifloroehanol

[rama david]

 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 ...


Rama David ...
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