[gmx-users] pdb file error

[Mark Abraham]

hhhh huan wrote:
> 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?

Capitalization and spelling are not optional parts of the English 
language. If you're asking for free help, you'll do best to make it easy 
for people to understand you, and to look competent enough to be worth 
helping. :-)

If you can generate an ester at all, then just swap the substituent 
groups and you'll have what you want. Or, read the documentation to see 
what this server is expecting as input for esters.

Mark