Re: [gmx-users] TIP4P water model

2012-09-23 Thread Justin Lemkul
On 9/23/12 2:28 PM, Ankita naithani wrote: Hi, So the commands from the beginning are appended below: pdb2gmx -vsite h -f 3HQN_tet_nolig.pdb -o system.gro (I choose option 6 for AMBER99sb-ILDN force field and then option 2 for TIP4P water model) editconf -f system.gro -o system_box.gro -c -

Re: [gmx-users] TIP4P water model

2012-09-23 Thread Ankita naithani
Hi, So the commands from the beginning are appended below: pdb2gmx -vsite h -f 3HQN_tet_nolig.pdb -o system.gro (I choose option 6 for AMBER99sb-ILDN force field and then option 2 for TIP4P water model) editconf -f system.gro -o system_box.gro -c -d 1.0 -bt dodecahedron genbox -cp system_box.g

Re: [gmx-users] TIP4P water model

2012-09-21 Thread Justin Lemkul
On 9/21/12 7:55 PM, Peter C. Lai wrote: Perhaps genion is not removing the dummy atoms properly? The problem is occurring with grompp before genion. We would need to see all the prior commands (exactly copied and pasted from the terminal) as well as the [molecules] section of the topology

Re: [gmx-users] TIP4P water model

2012-09-21 Thread Peter C. Lai
Perhaps genion is not removing the dummy atoms properly? On 2012-09-21 04:48:37PM +0100, Ankita naithani wrote: > Hi all, > > I am trying to begin a simulation of a protein. > > I am using AMBER99sb-ILDN force field and TIP4P water model. However, > I am facing a problem in the ion adding step.