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
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
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
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:
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
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
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
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
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