On 4/30/07, Sonali <[EMAIL PROTECTED]> wrote:
hi everybody, i am running Gromacs simulation with the protein 1f9b.pdb. I had earlier got some errors with the ligands present i.e FE, BCT and 3ID so i had run prodrg with BCT and 3ID but as prodrg server doesnot support for FE i had obtaine4d itp and top files for FE by pdb2gmx. and ommiting the HETATM portions i had obtained a gro file for 1f9b.pdb and later on had added the FE.gro , BCT.gro and 3ID.gro at the end of the 1f9b.gro file.then using pdb2gmx i got teh topology file which included the following at the end ; Include Position restraint file #ifdef POSRES #include "1f9b_with_ligand.itp" #include "FE.itp" #include "BCT.itp" #include "3ID.itp" #endif
You have included the topology files inside a IF function,,, unless you define -DPOSRES in your grompp those include files won't be read. So the cause of the error... place the FE, BCT and 3ID include lines out of the IF statement (which starts with #ifdef and ends with a #endif) I don't see a reason why you would put the include lines inside the IF statement. In case you are trying to do a position restrained MD, you need to list all the BCT, 3ID and FE atoms and the force with which you want to restrain them in the posre.itp file. ; Include water topology
#include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_A 1 FE 2 BCT 4 3ID 15 SOL 27303 but while running the grompp step i am getting error Fatal error: No such moleculetype FE i tried to move FE to another column like ions but thyen i get the same error with BCT and 3ID. Any suggestions are highly appreciated.
-- Venks ~ You will become rich and famous, unless you don't.
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