Re: [gmx-users] dialanine using charmm27 ff

2011-09-12 Thread Mark Abraham
On 10/09/2011 10:23 AM, Sandeep Somani wrote: Hi Mark It worked ! pdb2gmx is now properly processing the pdb, and moreover the potential energy from gmx is within 1.27 kJ/mol of that from Charmm. More on energy comparison shortly. However, further tinkering of the rtp and pdb file was

Re: [gmx-users] dialanine using charmm27 ff

2011-09-09 Thread Sandeep Somani
Hi Mark Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and renamed residue and atom names in pdb file. But pdb2gmx is still complaining about the terminal groups. It seems to have picked up ACE, but not CT3. pdb2gmx error message and modified pdb file are listed below.

Re: [gmx-users] dialanine using charmm27 ff

2011-09-09 Thread Mark Abraham
On 09/09/11, Sandeep Somani ssom...@gmail.com wrote: Hi Mark Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and renamed residue and atom names in pdb file. But pdb2gmx is still complaining about the terminal groups. It seems to have picked up ACE, but

Re: [gmx-users] dialanine using charmm27 ff

2011-09-09 Thread Sandeep Somani
Hi Mark It worked ! pdb2gmx is now properly processing the pdb, and moreover the potential energy from gmx is within 1.27 kJ/mol of that from Charmm. More on energy comparison shortly. However, further tinkering of the rtp and pdb file was required to generate the topology: 1. The original rtp

[gmx-users] dialanine using charmm27 ff

2011-09-08 Thread Sandeep Somani
Hi I am trying to set up a simulation for dialanine using charmm27 ff but am getting errors in pdb2gmx due to missing definitions in rtp file. I created the pdb file (below) using Charmm for the sequence ACE-ALA-ALA-CT3. pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE and

Re: [gmx-users] dialanine using charmm27 ff

2011-09-08 Thread Mark Abraham
On 9/09/2011 8:05 AM, Sandeep Somani wrote: Hi I am trying to set up a simulation for dialanine using charmm27 ff but am getting errors in pdb2gmx due to missing definitions in rtp file. I created the pdb file (below) using Charmm for the sequence ACE-ALA-ALA-CT3. pdb2gmx recognizes ALA

[gmx-users] dialanine

2006-06-08 Thread Debashis Dutta
Hi, I am seeking help in creating the .pdb file for a dialanine molecule using the databank. I have the parameters for a single alanine molecule. how do i go from here. Thanks Debashis ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] dialanine

2006-06-08 Thread Tsjerk Wassenaar
Hi Debashis, Parameters and .pdb file are different things. To generate a structure for dialanine you can use prodrg, pymol, write it by hand or search the web. If you want to use your own force field parameters you have to write a .itp file. Check the gromacs manual for that. TsjerkOn 6/8/06,