[gmx-users] gramicidin A

[pragya chohan]

----------------------------------------> Date: Sat, 3 Nov 2007 19:23:32 +1100> From: Mark.Abraham at anu.edu.au> To: gmx-users at 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> _______________________________________________> gmx-users mailing list gmx-users at gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/search before posting!> Please don't post (un)subscribe requests to the list. Use the> www interface or send it to gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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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