----------------------------------------> Date: Sat, 3 Nov 2007 19:23:32 +1100>
From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users]
gramicidin A>> pragya chohan wrote:>> hi>> I was trying to run pdb2gmx command
for gramicidin and noticed it has some D-amino acids.>> D-amino acids are
enantiomers of L-amino acids. Thus they're> topologically identical. So you can
use the same topology for them,> unless your force field has an interaction
that varies with chirality.> You know already whether your force field has one
of them, right? If it> doesn't, then you can just change some names.>>> I
generated .itp from prodrg server and included the above stated things in .rtp
file. But again when i ran pdb2gmx i got the same error..>> Residue 'DLE' not
found in residue topology database.>> See>
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database>>
You need to do some more work in understanding the purpose of running>
pdb2gmx, the way of using an .itp file, and/or understanding the .rtp> file
syntax. Check out http://wiki.gromacs.org/index.php/topology_file> and chapter
5 of the GROMACS manual.>> Mark>
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Thanks for your reply
I had already read the refered pages . I had made changes in the charge and
improper dihedrals. But pdb2gmx doesnt seem to recognise those amino acids
still.
No i dont know if my force field if chiraliy sensitive. Neways my system also
has Val in it.
The changes i made are
[ LEU ](ORIGINAL LEU)
[ atoms ]
N N -0.280 0
H H 0.280 0
CA CH1 0.000 1
CB CH2 0.000 2
CG CH1 0.000 3
CD1 CH3 0.000 4
CD2 CH3 0.000 5
C C 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA C
C O
-C N
CA CB
CB CG
CG CD1
CG CD2
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
CG CD2 CD1 CB
[ DLE ](INCORPORATED DLE)
[ atoms ]
N N 0.815 0
H H 0.041 0
CA CH1 0.189 1
CB CH2 0.000 2
CG CH1 0.000 3
CD1 CH3 0.000 4
CD2 CH3 0.000 5
C C 0.432 6
O O -0.559 6
[ bonds ]
N H
N CA
CA C
C O
-C N
CA CB
CB CG
CG CD1
Please help me.
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