Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-05-14 Thread Lara Bunte
Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:59 Montag, 7.Mai 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology On 5/7/12 2:54 PM, Lara

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-05-14 Thread Justin A. Lemkul
On 5/14/12 5:15 PM, Lara Bunte wrote: Hi All needed parameters for [ angles ] in the topology are defined in my .rtp file parametrization and also in the ffbonded.itp in the CHARMM27 folder. This still don't work. In the topology my [ angles ] block looks like [ angles ] ; aiajak

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-05-07 Thread Lara Bunte
- Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 21:59 Sonntag, 6.Mai 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology On 5/6/12 3:45 PM, Lara Bunte wrote: Hi You said: The blank lines

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-05-07 Thread Justin A. Lemkul
Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology On 5/6/12 3:45 PM, Lara Bunte wrote: Hi You said: The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. I let the lines empty and I got an error at the first grompp, before

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-05-06 Thread Lara Bunte
- Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-05-06 Thread Justin A. Lemkul
- Ursprüngliche Message - Von: Justin A. Lemkuljalem...@vt.edu An: Discussion list for GROMACS usersgmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-03-09 Thread Lara Bunte
take a look on it? Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 21:04 Mittwoch, 7.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-03-09 Thread Justin A. Lemkul
- Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-03-07 Thread Lara Bunte
@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-03-07 Thread Peter C. Lai
for helping me. Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-03-07 Thread Justin A. Lemkul
...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-03-07 Thread Peter C. Lai
Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; aiajak functc0c1

[gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-03-06 Thread Lara Bunte
Hi After pdb2gmx are in the [ angles ] section some lines missing and I am pretty sure that they are defined in my .rtp file in my force field folder. There are also just a few lines mission, most of the angles are in topology. I know the parameters so I can add it by hand to topology but what

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-03-06 Thread Justin A. Lemkul
Lara Bunte wrote: Hi After pdb2gmx are in the [ angles ] section some lines missing and I am pretty sure that they are defined in my .rtp file in my force field folder. There are also just a few lines mission, most of the angles are in topology. I know the parameters so I can add it by hand

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

2012-03-06 Thread Justin A. Lemkul
Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00