[gmx-users] regarding top file

[Mark Abraham]

On 12/22/2011 6:07 PM, priya thiyagarajan wrote:
> 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.

Please copy and paste actual input and output. I can't tell from the 
above whether you have mis-reported what error occurred or failed to 
follow the file format when you attempted step 1 of 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field 
(or likely both).

As Justin suggested yesterday, you should start with something simple. 
Get PRODRG to make a topology and coordinate file for glycine. Plan to 
name it something other than GLY. Convert that to .rtp and get that 
working with pdb2gmx. Then add complexity. You are trying to run before 
you understand much about walking yet.

>
> 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*.

Just about anything here could be wrong, including trying to use the 
prodrg.itp in a topology that formerly used an inappropriate force field.

Mark

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