Re: [gmx-users] grompp: invalid bond type error

2011-11-02 Thread Olivia Waring
Hi Justin and Mark, Thank you so much for your replies. Mark, would you mind clarifying what you mean? What exactly should I be looking for in the ffbonded.itp file? I'm not sure why those bonded parameters in particular were overridden... I didn't intend to modify anything! Perhaps it would

Re: [gmx-users] grompp: invalid bond type error

2011-11-02 Thread Justin A. Lemkul
Olivia Waring wrote: Hi Justin and Mark, Thank you so much for your replies. Mark, would you mind clarifying what you mean? What exactly should I be looking for in the ffbonded.itp file? I'm not sure why those bonded parameters in particular were overridden... I didn't intend to modify

Re: [gmx-users] grompp: invalid bond type error

2011-11-02 Thread Justin A. Lemkul
Olivia Waring wrote: Yes, it's the same error. About the bond types: should they be defined as opls_* in ffbonded.itp, aminoacids.rtp, both, or somewhere else entirely? The bonds are named in the aminoacids.rtp file, they are defined in ffbonded.itp. Use names in the .rtp, types in

[gmx-users] grompp: invalid bond type error

2011-11-01 Thread Olivia Waring
Dear Gromacs users, First of all, many thanks to Justin for his assistance with my previous question. I have defined a new residue type in the oplsaa force field, changing the aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try to preprocess, I get the following output:

Re: [gmx-users] grompp: invalid bond type error

2011-11-01 Thread Justin A. Lemkul
Olivia Waring wrote: Dear Gromacs users, First of all, many thanks to Justin for his assistance with my previous question. I have defined a new residue type in the oplsaa force field, changing the aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try to preprocess, I

Re: [gmx-users] grompp: invalid bond type error

2011-11-01 Thread Olivia Waring
Thank you so much for your quick reply! Below please find my topology file: ; Include forcefield parameters #include hautklein.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein_chain_1 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB

Re: [gmx-users] grompp: invalid bond type error

2011-11-01 Thread Justin A. Lemkul
Olivia Waring wrote: Thank you so much for your quick reply! Below please find my topology file: ; Include forcefield parameters #include hautklein.ff/forcefield.itp The problems you are experiencing are probably coming from this file, or perhaps somewhere else in your custom force

Re: [gmx-users] grompp: invalid bond type error

2011-11-01 Thread Mark Abraham
On 2/11/2011 8:32 AM, Olivia Waring wrote: Dear Gromacs users, First of all, many thanks to Justin for his assistance with my previous question. I have defined a new residue type in the oplsaa force field, changing the aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I