Re: [gmx-users] Extracting bond information from topol.tpr file using template.c

2012-09-19 Thread Erik Marklund
g_hbond does. 19 sep 2012 kl. 05.49 skrev Mark Abraham: > On 19/09/2012 12:49 PM, Amit Shavit wrote: >> Hello, >> >> I'm relatively new to GROMACS, and I need to write some of my own analysis >> tools using the template.c file. >> I have been able to figure out most of the structure of it, and h

Re: [gmx-users] Extracting bond information from topol.tpr file using template.c

2012-09-18 Thread Mark Abraham
On 19/09/2012 4:37 PM, Tsjerk Wassenaar wrote: g_bond.c / gmx_bond.c ? No, I checked earlier and it uses index groups. trjconv -pbc whole is no good either. Mark Cheers, Tsjerk On Sep 18, 2012 9:50 PM, "Mark Abraham" wrote: On 19/09/2012 12:49 PM, Amit Shavit wrote: > > Hello, > > I'm

Re: [gmx-users] Extracting bond information from topol.tpr file using template.c

2012-09-18 Thread Tsjerk Wassenaar
g_bond.c / gmx_bond.c ? Cheers, Tsjerk On Sep 18, 2012 9:50 PM, "Mark Abraham" wrote: On 19/09/2012 12:49 PM, Amit Shavit wrote: > > Hello, > > I'm relatively new to GROMACS, and I need ... The easiest way to learn how to use the information in the .tpr is to work by analogy from an existing t

Re: [gmx-users] Extracting bond information from topol.tpr file using template.c

2012-09-18 Thread Mark Abraham
On 19/09/2012 12:49 PM, Amit Shavit wrote: Hello, I'm relatively new to GROMACS, and I need to write some of my own analysis tools using the template.c file. I have been able to figure out most of the structure of it, and how the C Structs are used. That is to say, I can successfully retrieve pa

Re: [gmx-users] Extracting bond information from topol.tpr file using template.c

2012-09-18 Thread Peter C. Lai
I forgot to mention that the bond info should be in the .tpr file somewhere as it was processed from the topology and I think gmxdump will also show the connectivities. On 2012-09-18 10:49:25PM -0400, Amit Shavit wrote: > Hello, > > I'm relatively new to GROMACS, and I need to write some of my ow

Re: [gmx-users] Extracting bond information from topol.tpr file using template.c

2012-09-18 Thread Peter C. Lai
The topol.top/.itp files have the pairwise bond information. On 2012-09-18 10:49:25PM -0400, Amit Shavit wrote: > Hello, > > I'm relatively new to GROMACS, and I need to write some of my own analysis > tools using the template.c file. > I have been able to figure out most of the structure of it,

[gmx-users] Extracting bond information from topol.tpr file using template.c

2012-09-18 Thread Amit Shavit
Hello, I'm relatively new to GROMACS, and I need to write some of my own analysis tools using the template.c file. I have been able to figure out most of the structure of it, and how the C Structs are used. That is to say, I can successfully retrieve particle positions, residue IDs, residue names,