Re: [gmx-users] rtp entry

David van der Spoel wrote: ASHWINI JAYAPRAKASH wrote: Hi Mark, I have used pdb2gmx to create the topology file with the option of -missing,also I have deleted the HEATOM that were there in the pdb file. Will these be a problem later? Now when I run grompp I am getting the error "Atomtype

Re: [gmx-users] rtp entry

ASHWINI JAYAPRAKASH wrote: Hi Mark, I have used pdb2gmx to create the topology file with the option of -missing,also I have deleted the HEATOM that were there in the pdb file. Will these be a problem later? Now when I run grompp I am getting the error "Atomtype 'opls_135' not found!"

Re: [gmx-users] rtp entry

Hi Mark, I have used pdb2gmx to create the topology file with the option of -missing,also I have deleted the HEATOM that were there in the pdb file. Will these be a problem later? Now when I run grompp I am getting the error "Atomtype 'opls_135' not found!" .

Re: [gmx-users] rtp entry

ASHWINI JAYAPRAKASH wrote: Hi Mark, I have changed the atom name in the co-ordinate file. Now I get an error saying : Residue "pop" not found in residue database My co-ordinate file consists of protein, popc and sol. Do I have to add the itp files of popc and sol to the rtp file. Only i

Re: [gmx-users] rtp entry

Hi Mark, I have changed the atom name in the co-ordinate file. Now I get an error saying : Residue "pop" not found in residue database My co-ordinate file consists of protein, popc and sol. Do I have to add the itp files of popc and sol to the rtp file. Thanks, Aj Mark Ab

Re: [gmx-users] rtp entry

ASHWINI JAYAPRAKASH wrote: Hi Mark, Thank you for your valuable suggestion.I did go through the manual, but I want to confirm if I need to add the atom CA in the ffoplsaa.rtp file, and if so I am not sure what the appropiate Type of angles, Type of proper dihedrals, Type of improper dihedra

[gmx-users] rtp entry

Hi Mark, Thank you for your valuable suggestion.I did go through the manual, but I want to confirm if I need to add the atom CA in the ffoplsaa.rtp file, and if so I am not sure what the appropiate Type of angles, Type of proper dihedrals, Type of improper dihedrals I have to enter. If

Re: [gmx-users] rtp entry

ASHWINI JAYAPRAKASH wrote: Hi, I am a new gromacs user and have problems creating a topology file using the pdb2gmx command for simulating a six helix bundled alamethecin in lipid bilayer. when I use the command : pdb2gmx -f almN6start -o almN6start.gro -p almN6start.top I get the error :

[gmx-users] rtp entry

Hi, I am a new gromacs user and have problems creating a topology file using the pdb2gmx command for simulating a six helix bundled alamethecin in lipid bilayer. when I use the command : pdb2gmx -f almN6start -o almN6start.gro -p almN6start.top I get the error : Program pdb2gmx, VERSION 3.3.