On 11/20/17 12:01 PM, RAHUL SURESH wrote:
Dear Justin
On adding this to the rtp file I received the error "Atom in residue CU 1
was not found in rtp entry CU with 1 atoms
while sorting atoms". for the pdb2gmx command.
Also the warning state
* "Warning: Starting residue CU1 in chain not i
Dear Justin
On adding this to the rtp file I received the error "Atom in residue CU 1
was not found in rtp entry CU with 1 atoms
while sorting atoms". for the pdb2gmx command.
Also the warning state
* "Warning: Starting residue CU1 in chain not identified as
Protein/RNA/DNA.Problem with chai
On 11/20/17 11:05 AM, RAHUL SURESH wrote:
Dear Justin
Sorry for the inconvenience. Tried every possible way and couldn't find any
proper way to add datas into merged.rtp. As you have suggested, Yes i have
made some incorrect format entry.
Can you please guide me to make a valid entry in rtp fi
On 11/20/17 11:13 AM, Justin Lemkul wrote:
On 11/20/17 11:05 AM, RAHUL SURESH wrote:
Dear Justin
Sorry for the inconvenience. Tried every possible way and couldn't
find any
proper way to add datas into merged.rtp. As you have suggested, Yes i
have
made some incorrect format entry.
Can yo
Dear Justin
Sorry for the inconvenience. Tried every possible way and couldn't find any
proper way to add datas into merged.rtp. As you have suggested, Yes i have
made some incorrect format entry.
Can you please guide me to make a valid entry in rtp file? Which one is the
right format. I have sear
On 11/17/17 2:30 AM, RAHUL SURESH wrote:
Dear Justin
I have tried various measures to over come it.
1. I added Cu in merged.rtp and still the error prevails.
*Error: Fatal error:in .rtp file in residue ions at line:Cu*
This appears to indicate an incorrectly formatted .rtp entr
Dear Justin
I have tried various measures to over come it.
1. I added Cu in merged.rtp and still the error prevails.
*Error: Fatal error:in .rtp file in residue ions at line:Cu*
2. I added TER in the pdb file and still the same error. Then I removed Cu
from merged.rtp and again error
On 11/16/17 1:53 PM, RAHUL SURESH wrote:
Dear Justin
Why is there no aminoacids.rtp file in charmm36ff?
Because the way the CHARMM topology and parameter files are constructed
makes it nearly impossible to actually write out only certain types of
molecules, we lumped (almost) everything in
Dear Justin
Why is there no aminoacids.rtp file in charmm36ff?
As mentioned before I have added the metal ion parameters in nonbonded.itp,
ions.ipt and atomtypes.itp. While performing simulation using the command *"gmx
pdb2gmx -f cu.pdb -o cu.gro -p cu.top" *I receive the following error
"Residue
That’s good enough to perform the simulation. Thank you Justin.
On Thu, 16 Nov 2017 at 6:33 PM, Justin Lemkul wrote:
>
>
> On 11/16/17 4:12 AM, RAHUL SURESH wrote:
> > On Wed, Nov 15, 2017 at 6:58 PM, Justin Lemkul wrote:
> >
> >>
> >> On 11/15/17 6:44 AM, RAHUL SURESH wrote:
> >>
> >>> Hell
On 11/16/17 4:12 AM, RAHUL SURESH wrote:
On Wed, Nov 15, 2017 at 6:58 PM, Justin Lemkul wrote:
On 11/15/17 6:44 AM, RAHUL SURESH wrote:
Hello users
I am performing Metal-protein interactions with Charmm36ff using gromacs.
The metals under study are Cu and Ag in +2 state. Is it sufficient
On Wed, Nov 15, 2017 at 6:58 PM, Justin Lemkul wrote:
>
>
> On 11/15/17 6:44 AM, RAHUL SURESH wrote:
>
>> Hello users
>>
>> I am performing Metal-protein interactions with Charmm36ff using gromacs.
>> The metals under study are Cu and Ag in +2 state. Is it sufficient to add
>> the topology,i.e th
On 11/15/17 6:44 AM, RAHUL SURESH wrote:
Hello users
I am performing Metal-protein interactions with Charmm36ff using gromacs.
The metals under study are Cu and Ag in +2 state. Is it sufficient to add
the topology,i.e the necessary parameters (LJ-potentials) in nonbonded.itp
and ions.itp alone
Hello users
I am performing Metal-protein interactions with Charmm36ff using gromacs.
The metals under study are Cu and Ag in +2 state. Is it sufficient to add
the topology,i.e the necessary parameters (LJ-potentials) in nonbonded.itp
and ions.itp alone?
In case of nonbonded.itp file, i find char
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