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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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