n of gromacs than you have at the moment. What
> version do you currently use?
>
> Erik
>
> On 12 Jun 2013, at 12:56, Nikunj Maheshwari
> wrote:
>
> > Yes I checked. do_dssp has no -ver option.
> > I also found out this link
> >
> > https://gerrit.gromacs
ged at some point and it
> took a while before do_dssp adapted to that. If your do_dssp is lacking the
> -ver option then I'm quite confident that it uses the old syntax, which
> doesn't work with the newer versions (v. 2.0+ I think) of dssp.
>
> Erik
>
> On 12 Jun
The location of dssp is /usr/local/bin/dssp
On Wed, Jun 12, 2013 at 3:43 PM, Mark Abraham wrote:
> Right. And what is its location?
> On Jun 12, 2013 11:17 AM, "Nikunj Maheshwari"
> wrote:
>
> > Yes I did searched. But for most people, there were issues regardin
ed.
>
> Erik
>
> On 12 Jun 2013, at 10:31, Nikunj Maheshwari
> wrote:
>
> > Dear all,
> >
> > I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
> > I am trying to use it for do_dssp command but get the following error
> each
> >
Dear all,
I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
I am trying to use it for do_dssp command but get the following error each
time:
"Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 >
/dev/null 2> /dev/null
"
Is there any way to recti
Alternatively, you can use editconf -f (tpr file) -o (pdb file) to convert
.gro to .pdb, and then use the visualization tools such as Pymol to view it.
On Tue, May 21, 2013 at 1:01 AM, Vishal Kumar Jaiswal
wrote:
> Vmd can visualise a GRO file directly without .tpr . I use it to visualise
> gro
t; -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> > -Original Message-
> > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> > boun...@gromacs.org] On Behalf Of Nikunj Mahe
Dear all,
I am trying to see the folding of a 89 aa peptide. So I am setting up the
system from linear conformation.
I gave the following commands to build the box and add the solvent
molecules.
editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro
genbox -cp outbox.gro -cs spc216.gro
Heme (HIS1) #Works. total charge= -17.000
So shall I go ahead with any of the option except 1, or use -ignh?
On Tue, Apr 30, 2013 at 3:33 PM, Justin Lemkul wrote:
>
>
> On 4/30/13 2:59 AM, Nikunj Maheshwari wrote:
>
>> Dear all,
>>
>> I got an error while usin
Dear all,
I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
output.gro)
I used 13. GROMOS 53a6 force field
"Fatal error:
Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while
sorting atoms.
For a hydrogen, this can be a different protonation state, or it
mi
9, 2013 at 6:42 PM, Mark Abraham wrote:
> On Tue, Apr 9, 2013 at 10:44 AM, Nikunj Maheshwari
> wrote:
> > Thats true with our case as well. The spacing was very small, and we got
> > almost 70 replicas for our protein between 280-410K.
> > That's why, we are thi
eted.
>
> Erik
>
> On 9 Apr 2013, at 10:01, Nikunj Maheshwari
> wrote:
>
> > How did you get the final temperature spacing for the run? Did you get
> the
> > fitted values using polynomial fit?
> > Was the run completed?
> >
> > On Tue, Apr 9, 2013
How did you get the final temperature spacing for the run? Did you get the
fitted values using polynomial fit?
Was the run completed?
On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund wrote:
> I've tried one with 666 aa, but with no publishable results.
>
> On 9 Apr 2013, at
Dear all...
Does anyone has any idea what is the maximum protein size for which a
successful REMD run has taken place?
We have went through lots of research papers, but could not find any
protein/peptide above 100 aa related to REMD.
We have a protein of 292 aa.
Thanks.
--
gmx-users mailing list
Hi. Glad to know that your REMD was successful. We are trying to do the
same, but are stuck in between.
Can you tell us, how did you got the temperature spacing?
Thanks
On Tue, Apr 9, 2013 at 11:59 AM, Shine A wrote:
> Respected sir,
>
> I successfully completed REMD sim
>
> http://folding.bmc.uu.se/remd/ this may help you.
>
>
> With best regards
>
>
> On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari <
> nixcrazyfor...@gmail.com
> > wrote:
>
> > Dear all,
> >
> > We are stuck at the last stage of running a successful R
Dear all,
We are stuck at the last stage of running a successful REMD.
We have obtained average potential energy by fitting the energy values from
initial MD.
We want to get the temperature spacing for 72 replicas, starting from 280K.
We have gone through numerous papers, but none of them explain
Dear all...
We ran REMD simulations for 36 replicas. We got an error which stopped the
whole simulation.
"
Reading file md21.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Reading file md24.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
---
>
> Mark
>
> On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari <
> nixcrazyfor...@gmail.com> wrote:
>
> > I think determining k in the equation is not clear. How is it related to
> a
> > system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given
>
at 11:24 AM, Nikunj Maheshwari <
> nixcrazyfor...@gmail.com> wrote:
>
> > Dear all.
> >
> > We are trying to run REMD on two proteins : 292 and 44 aa residues using
> > GROMACS 4.6.
> > We are unable to obtain the temperature spacing using REMD temperature
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