On 1/11/15 11:08 AM, Siddhesh Kamat wrote:
Hello everyone,
links to attchments:
https://drive.google.com/file/d/0B83MUXW1ifjQLVJoalhNR1FRczg/view?usp=sharing
( itp file)
Your topology format is wrong. You don't have a residue name column:
; nr type resnr atom cgnr charge
Hello everyone,
links to attchments:
https://drive.google.com/file/d/0B83MUXW1ifjQLVJoalhNR1FRczg/view?usp=sharing
( itp file)
https://drive.google.com/file/d/0B83MUXW1ifjQcWR5Ny1UczZxMUk/view?usp=sharing
(top file)
Regards,
Siddhesh Kamat
On Sun, Jan 11, 2015 at 11:00 AM, Justin Lemkul wrote:
On 1/11/15 10:57 AM, Siddhesh Kamat wrote:
Hello everyone,
Thanks for the prompt reply. I have attached the .itp and .top files of
MPNA(monoprotic napthenic acid). This is the error I get on energy
minimisation:
The mailing list does not accept attachments. That's why I said provide a link
Hello everyone,
Thanks for the prompt reply. I have attached the .itp and .top files of
MPNA(monoprotic napthenic acid). This is the error I get on energy
minimisation:
command line
gmx grompp -f minim.mdp -c MPNA_solv.gro -p topol.top -o em.tpr
Back Off! I just backed up mdout.mdp to ./#mdout.md
On 1/11/15 10:23 AM, Siddhesh Kamat wrote:
Hello everyone,
I am working on a monoprotic Napthenic acid(a simple straight chain one
C29H59COOH). I made the .itp file and used PRODRG for the .gro file. I am
unable to energy minimise the system after adding TIP4P water. The error I
am getting is
Hello everyone,
I am working on a monoprotic Napthenic acid(a simple straight chain one
C29H59COOH). I made the .itp file and used PRODRG for the .gro file. I am
unable to energy minimise the system after adding TIP4P water. The error I
am getting is 'net charge is non zero and the number it gives
On 1/10/15 7:36 PM, Jonathan Saboury wrote:
Not likely Xavier. It isn't a single water acting unusual. It is many
waters (probably all) and all biotins making odd angles/lengths.
Nevertheless I tried the suggestion and I am getting different results, but
not sure if they are good results.
"vm
On 1/11/15 9:01 AM, mah maz wrote:
Hi Justin,
That's right in the .edr I have more than these 4 terms, I just mentioned
the terms related to energy of the system.The output file is a large one
Those aren't the only terms related to the energy, and "conserved energy" is
actually a thermostat
On 1/11/15 1:32 AM, elham tazikeh wrote:
Dear Mark/Leila
thanks for your reply
i knowing that for seeing all processes have done in my terminal page, i
must to use *history* tool
but *history* just give us main commands in my terminal page...i want to
see all processes with details (e.g. which
Hi Justin,
That's right in the .edr I have more than these 4 terms, I just mentioned
the terms related to energy of the system.The output file is a large one
not in a proper format to be sent, but can be attached if possible.
That was a great deal of help up to this point.
Thank you very much!
Rega
The warning of grompp says you have two charge groups (bound groups from a
molecule) at 7 nm, while the cutoff of theses interactions is 1 nm! This most
likely reflects a broken molecule …
Visualising your system indicates it is broken all over the place at the PBC.
Make your molecule whole f
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