[gmx-users] Re: It consults in Gromacs (Carolina, Venezuela)

[David van der Spoel]

Carolina Silva wrote:
> Many greetings
> Please excuse my level for English. I am learning it
> I am also trying to learn to handle the program GROMACS
> 
> I want to simulate a pure ethylbenzene mixture (first step ) but I hoped
> to obtain it from phenylalanine, so that I saw that the blocks of
> construcion of molecules of gromacs are of amino acids and the structure
> of the phenylalanine is very similar to the one of ethylbenzene.
> 
> when executing (pdb2gmx -f phe2.pdb -p phe2.top -o phe2.gro -n phe2.ndx,
> force field: 4, GROMOS96 53a5) the atoms of H and O were not added to
> each molecule.
> This treating pdb like a chain and not like 6 molecules:
>   chain  #res #atoms
>   1 ' '     6    102
> Adds the H and O single to the first molecule:
> Warning: Long Bond (18-20 = 1.26907 nm)
> Warning: Long Bond (35-37 = 1.44758 nm)
> Warning: Long Bond (52-54 = 1.45013 nm)
> Warning: Long Bond (69-71 = 1.53424 nm)
> Warning: Long Bond (86-88 = 0.560715 nm)
> Can you help me about this uncertainty?
Please ask such questions on the mailing list.

You can try the PRODRG webserver for a start. Then I'd advise you to 
read chapter 5 in the manual.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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