[gmx-users] regarding top file

[priya thiyagarajan]

hello sir,
i dono what i did was correct or not. But i did it.
please tell me what i did was correct or not,,
i tried two different ways to generate my top file.


first i did prodrg for my whole lipopeptide and got its itp . pdb and gro
file.
then i included information about atomtype, bond, pairs ,dihedrals from
this prodrg.itp into charmm27 forcefield rtp.
And also added DRG as lipid in residuetype.dat..
then i tried
*pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh*

but i got error as
* No atom found in .rtp file in residue moleculetype.*

so i though of using pdb file obtained from prodrg as input and repeated
the step.
But still i am getting the same error.

second way
i took one topology file generated for some protein and edited it.
and i included my prodrg.itp file using include mechanism
then set box to that prodrg.gro file and added water. And used that top
file which i edited since it contain all information about my pdb.
even my SOL molecules got  written in that topology file.
then i viewed that proteinwater.pdb file using pymol.
when i go for energy minimisation i got error
*atomtye CH3 not found*.

please help me with your answer..

Thanking you,
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