I would use -dump to extract only the last frame,
I believe that what your are doing is saving your trajectory in a pdb file.
On 14 May 2016 at 16:21, Mark Abraham wrote:
> Hi,
>
> Sure, but if you have a million frames, then you are probably doing
> something other than what you want or shoul
ption.
Francesco
On 29 April 2016 at 17:12, Justin Lemkul wrote:
>
>
> On 4/29/16 12:08 PM, Francesco Carbone wrote:
>
>> Good afternoon,
>>
>> I'd like to run a dynamics with a protein (2bhl.pdb) and its substrate
>> (Glucose-6-phosphate ) to observe ho
Good afternoon,
I'd like to run a dynamics with a protein (2bhl.pdb) and its substrate
(Glucose-6-phosphate ) to observe how mutants affects the binding.
Following Justin tutorial (thank you Justing for providing it), I use
PRODRG to generate the topology for G6P and I then included in the prote
You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later.
Cheers,
Fra
On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote:
> Hi Irem,
>
> Check the structure in nvt_water_frozen.tpr:
>
> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
>
> Cheers,
>
> Tsjerk
> On Mar 31, 2016 0
12:49, Justin Lemkul wrote:
>
>
> On 2/17/16 7:11 AM, Francesco Carbone wrote:
>
>> Thank you Justin,
>>
>> I'm not a pro in C, but I think that in the code, the omega angle is
>> defined as CA-C-N-CA (Bug #953 discussed this)
>> ...
>> dl[i].j0
the trajectory?
Regards,
Francesco
On 16 February 2016 at 17:53, Justin Lemkul wrote:
>
>
> On 2/16/16 12:40 PM, Francesco Carbone wrote:
>
>> Thank you again for the quick response,
>>
>> I read that, but I'm calculating the omega angle which shouldn't b
On 16 February 2016 at 17:30, Justin Lemkul wrote:
>
>
> On 2/16/16 12:26 PM, Francesco Carbone wrote:
>
>> Thank you Justin,
>>
>> I selected the atoms (CA-C-N-CA) for the dihedral I want and check with
>> "gmx angle" (gmx angle -f -n ciao.ndx -type dih
>
> On 2/16/16 10:16 AM, Francesco Carbone wrote:
>
>> good afternoon,
>>
>> I'm trying to study the values of the omega dihedral (peptide bond) for a
>> specific Proline in my protein.
>> This Proline is known to exists in both cis and trans conformation(cis
&
good afternoon,
I'm trying to study the values of the omega dihedral (peptide bond) for a
specific Proline in my protein.
This Proline is known to exists in both cis and trans conformation(cis
while binding).
In the pdb I used as starting point for the simulation (2bhl.pdb) the
Proline (172) is i
I use to have the same problem and in my case it was cause by the fact that
I was using a different tpr file (cleaned from water).
When I started using the "untouched" tpr file (the one used during the
simulation) everything went fine using trjconv and the -dump option.
Fra
On 3 February 2016 at
ted, and -output (which is optional)
> just specifies extra groups on top of this to calculate the area for.
>
> As for the legends for the extra columns, no one has just had the time to
> implement nice output for all possible cases.
>
> Best regards,
> Teemu
>
> On W
Good afternoon,
I calculated the residue area (-or) over my trajectory, but I have trouble
understanding the output.
With gromacs 4.6 I obtain a clean file:
residue value standard dev
27 4.654781.19505
280.990566 0.966795
29 1.77202 0.6297
good afternoon all,
I'm having problems in running a "well-tempered parallel tempering
metadynamics" with gromacs 5.
The problem is that I don't understand how to set -multi based on the cpu I
have (the cluster has both 12 and 16 cpu x node).
If I want to run 10 replicas spread over 160 cores I s
When you open the file you can set "first frame", "last frame"and "stride".
Try to increase the stride to skip frames.
On 10 September 2015 at 17:25, Homa rooz wrote:
> Hi guys!
> I have had a problem with VMD when reads frames on xtc file. It stops
> suddenly. It seemed VMD is working out o
es 171 263 201 202 205 395 365 239 360 258 are part of "Protein".
Cheers,
Francesco
On 4 September 2015 at 12:12, Teemu Murtola wrote:
> Hello,
>
> On Fri, Sep 4, 2015 at 1:51 PM Francesco Carbone
> wrote:
>
> > I've recently started using gromacs 5.0.4 and I
es 171 263 201 202 205 395 365 239 360 258 are part of "Protein".
Cheers,
Francesco
On 4 September 2015 at 12:12, Teemu Murtola wrote:
> Hello,
>
> On Fri, Sep 4, 2015 at 1:51 PM Francesco Carbone
> wrote:
>
> > I've recently started using gromacs 5.0.4 and I
Good morning,
I've recently started using gromacs 5.0.4 and I can't make"gmx sasa" to
recognise non-standard groups for the -output flag.
I have three groups (G6P, Co-enzyme and strNADP+; all subset of the dimer )
and every time I specify one of the three with "-output" flag I get:
"Inconsistency i
Dear Gromacs users,
I'm trying to see the part of a protein that are accessible to an average
size antibody and to do that I'm calculating the Solvent Accessible Surface
Area using a bigger probe (-probe 1.5 ).
The problem is that every time (and with different machines) I have
"Segmentation fault
Dear Gromacs users,
I'm trying to see the part of a protein that are accessible to an average
size antibody and to do that I'm calculating the Solvent Accessible Surface
Area using a bigger probe (-probe 1.5 ).
The problem is that every time (and with different machines) I have
"Segmentation fault
Good afternoon,
I have some trajectories of coarse-graned (CG) simulations obtained using
the UNRES force field (not implemented in GROMACS).
I'd like to apply the analysis protocol that I generally use for gromacs
trajectories also to these one, but because there are no native tools, I
was think
hi Negar,
I'm doing a similar work, but with another protein and what I did was to
mutate the wild-type using mutmodel (Martin et al., 2002).
In my case I had more than 200 mutants and only the wt pdb was available.
cheers,
Fra
On 3 June 2014 13:19, Negar Parvizi wrote:
> Dear Gromacs users
>
21 matches
Mail list logo
