[gmx-users] pdb file error

[Justin A. Lemkul]

Are you using text-based entry?  I've found that to be a lot more difficult than
drawing the molecule using the JME interface.  I've never had a problem with
JME, and my esters have always come out alright.

-Justin

Quoting hhhh huan <scottiehuan at yahoo.com>:

> hi GMX users,
>
> i am facing some problems to obtain the proper pdb
> file OF CCCCCCCCC=CCCCCOC=OCCCCCCCC=CCC=CCCCC from
> DUNNDEE PRO DRG server...
> the correct pdb file should be .....COOC...
> it is a ester group but the pdb i obtained was
> ..CCCOCOCC...
> i tried to subtitude both acid part double bond to
> single bond.., i managed to get the
> ...COOC...arragement in pdb file..
> so i wonder there is any other way to obtain the pdb
> file which can be used in GROMACS o other solution to
> settle this?
>
> thanks for any helps n comments.
>
>
>
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Justin A. Lemkul
Graduate Research Assistant
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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