<r><br/> Thanks for the tip. I should have updated earlier, the Segmentation error is not showing up now. When I run "mdrun_openmm" using "gdb debugger", the commands go through fine except for a line in the md.log - <br/> <br/> agb parameter file line=<> is being skipped<br/> <br/> From an earlier ...

I did have the GMXLIB set to the full pathname. I also added the full pathname to PATH. Not sure if that would really matter. But now the nature of the problem seems to have changed to "Segmentation fault" when I use the mdrun_openmm.

<t><br/> Thanks Peter for the reply. There were a few different versions of gromacs installed on our system. I just removed the redundant ones that I had access to. <br/> <br/> It is not very clear, from the error message on the log file, which directory it is seeking in - <br/> <br/> Could not find...

<t><br/> I have the params.agb file in the "gromacs/share/gromacs/top". The md.log still gives the error - <br/> <br/> Could not read agb file. GBSA is being omitted.<br/> <br/> I am running with CUDA, 64 bit linux with PR4.<br/> <br/> Any suggestion on what I could do?<br/> <br/> Thanks, <br/> <br/...

<t><br/> Update on this is that, I just commented out the section in *.top file that's looking for "spc.itp". With this, I continued with rest of the simulation and no errors appeared. The graphical output as seen in VMD appears normal. <br/> <br/> I am not sure if doing this is legitimate? I am als...

<r><br/> I am setting up an implicit solvent simulation using amber force field. <br/> <br/> When I want to do an energy minimization, I get an error - <br/> <br/> Fatal error:<br/> [ file spc.itp, line 37 ]:<br/> Atom index (1) in bonds out of bounds (1-0).<br/> This probably means that you have in...

Great. Thanks. I have no idea how I could have missed that.

Thanks again,
VJ

I should have mention that too in my earlier post. Sorry. My pdb files does have the corresponding atoms -

ATOM 262 N ALA 35
aTOM 263 CA ALA 35
ATOM 264 C ALA 35
ATOM 265 O ALA 35

VJ

<t><br/> I was trying to use amberff03 force field with Gromacs on CUDA. I have renamed the atoms in the pdb file as per the amber standards following the protocol in amberff*.rtp<br/> <br/> I get the following error - <br/> <br/> Program pdb2gmx, VERSION 4.0.5<br/> Source code file: genhydro.c, lin...

Thanks Peter,

We are working on the force field porting and hope to be completed with it shortly.

For the energy, I am using PR4, but may be I should double check my flag settings.

Thanks Again,
VJ