[gmx-users] gramicidin A

[Mark Abraham]

pragya chohan wrote:

> I had already read the refered pages .

Great.

> I had made changes in the charge and improper dihedrals. 

Since you don't need to do this, it's best not to do this.

> But pdb2gmx doesnt seem to recognise those amino acids still. 

So your .rtp is broken somehow. Probably you broke it doing the above. 
Did you edit the same .rtp file that pdb2gmx is finding at run-time? 
Check $GMXLIB

> No i dont know if my force field if chiraliy sensitive. 

Well, if you did, you'd know whether you needed a topology for each 
enantiomer. I'm not asking you to find this out to waste your time - the 
exercise will teach you valuable things :-) The literature references 
for all the force fields are in the GROMACS manual.

> Neways my system also has Val in it.

Great. That doesn't matter at all.

> 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.

At the very least your charge groups are broken, and your impropers are 
missing. Read chapter 5 of the manual.

If you want to see what changes you have done, save the old .rtp file 
before you edit and look at the output of "diff old.rtp new.rtp"

Mark