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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