On 8/23/18 8:12 AM, Amir Zeb wrote:
Thanks Justin,
I have followed what did you suggest for .rtp entry in merged.rtp file of
charmm36 ff.
But i could not make .hdb file for ALY. Where can i find the H-information
for ALY to insert them in merged.hdb file of charmm36 ff?
Look at existing
Thanks Justin,
I have followed what did you suggest for .rtp entry in merged.rtp file of
charmm36 ff.
But i could not make .hdb file for ALY. Where can i find the H-information
for ALY to insert them in merged.hdb file of charmm36 ff?
Amir
On Thu, Aug 23, 2018, 9:02 PM Justin Lemkul wrote:
>
>
On 8/23/18 7:52 AM, Bratin Kumar Das wrote:
Hi
You can see that only the problem is coming from hydrogen. So in pdb2gmx
command use -ignh so that it ignores the hydrogen. If you use this this
WARNING will not come.
That's not true. The -ignh option ignores H atoms in the input
On 8/23/18 6:30 PM, Amir Zeb wrote:
Thanks Justin,
Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/ and
generated the parameters for KAC.
Do not generate parameters in this way. You will have a mixture of
highly optimized protein parameters for all other residues,
Hi
You can see that only the problem is coming from hydrogen. So in pdb2gmx
command use -ignh so that it ignores the hydrogen. If you use this this
WARNING will not come.
On Fri, Aug 24, 2018 at 4:00 AM, Amir Zeb wrote:
> Thanks Justin,
>
> Actually I used Parachem CGenFF server
Thanks Justin,
Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/ and
generated the parameters for KAC.
The merged.rtp file was modified by adding the KAC parameters
That issue fixed, but now I'm getting the following warning which
ultimately results in fatal error.
WARNING:
On 8/22/18 5:26 AM, Bratin Kumar Das wrote:
Hi
In your tool.top file the particular lys molecule residue name you have
to modify. Then it will work..Actually grompp can't find the molecule in
the topology.
The error has nothing to do with grompp. The topology was never created
because
Hi
In your tool.top file the particular lys molecule residue name you have
to modify. Then it will work..Actually grompp can't find the molecule in
the topology.
On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, <177cy500.bra...@nitk.edu.in>
wrote:
> Hi
> In your tool.top file the
Hi
In your tool.top file the particular lys molecule residue name you have
to modify. Then it will work..Actually grompp can't find the molecule in
the topology.
On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, wrote:
> Hi gromacs users,
>
> I want to simulate a protein where one of the lysine
