How will I define ZN(HOH) in aminoacids.hdb?
2014-04-05 9:12 GMT+03:00 Ahmet yıldırım :
> You said "You likely need to put the Zn(HOH) complex in the same chain as
> the protein, and this is probably another reason for creating a Zn(HOH)
> residue and defining it as protein".
> How will I do wha
You said "You likely need to put the Zn(HOH) complex in the same chain as
the protein, and this is probably another reason for creating a Zn(HOH)
residue and defining it as protein".
How will I do what you say?
2014-04-05 7:13 GMT+03:00 Justin Lemkul :
>
>
> On 4/4/14, 11:58 PM, Ahmet yıldırım w
Hi Richa,
I was not able to get exactly what I wanted. As you know the g_sham output
does not give you the energy Vs PC information, rather it gives energy Vs
bin index information. So, the problem is how to transform bin index
information into PC values.
As I was not much interested in exact PC
On 4/4/14, 11:58 PM, Ahmet yıldırım wrote:
Hi,
The distance I have set in specbond.dat must correct (req from Table 1). I
get them from literature.Please see this link:
http://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CC0QFjAA&url=http%3A%2F%2Fpubmedcentra
Hi,
The distance I have set in specbond.dat must correct (req from Table 1). I
get them from literature.Please see this link:
http://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CC0QFjAA&url=http%3A%2F%2Fpubmedcentralcanada.ca%2Fpicrender.cgi%3Fartinstid%3D148221
Hi Klniu,
I am having the similar problem as you had two years ago. May I ask that if
you had solved the problem? Would you mind share with us how you solved it?
I'd very appreciate it!
C.G
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On 4/4/14, 1:46 PM, Ahmet yıldırım wrote:
Dear Justin,
These parameters are present in literature. I think these bonds/parameters
are correctly generated. You said "The previous topology output suggests
not, because ZN is not renamed to ZNW". I do not know what to do.
Probably because the
Dear Justin,
These parameters are present in literature. I think these bonds/parameters
are correctly generated. You said "The previous topology output suggests
not, because ZN is not renamed to ZNW". I do not know what to do.
I added the OZ-HZ bond in ffbonded.itp. Unfortunately I get the same
Thank you Justin,
I will appreciate the help with this doubt, of the reference group, that is not
0 , is 26 in the index file,
or the appropiate definition of the reference group thanks
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On 4/4/14, 9:25 AM, Ahmet yıldırım wrote:
Dear Justin,
Firstly, I renamed HETATM 2068 O HOH A1001 in pdb. This water is bound to
Zn.
its new name:
HETATM 2068 OZ OWZ A1001
Zn is bound to three Histidine atoms (two NE2 atoms and one ND1 atom) and a
water molecule in carbonic anhydrase as I
On 4/4/14, 9:17 AM, Andres Ortega Guerrero wrote:
i am aggre with you Justin
But when i used pull_group0_name= protein2pull
this warning appear : WARNING 1 [file pull_npt.mdp, line 70]:
Unknown left-hand 'pull_group0_name' in parameter file
and if i used
pull-coord1-groups = 26 1
Dear Justin,
Firstly, I renamed HETATM 2068 O HOH A1001 in pdb. This water is bound to
Zn.
its new name:
HETATM 2068 OZ OWZ A1001
Zn is bound to three Histidine atoms (two NE2 atoms and one ND1 atom) and a
water molecule in carbonic anhydrase as I said before. I did the following
changes on a
i am aggre with you Justin
But when i used pull_group0_name= protein2pull
this warning appear : WARNING 1 [file pull_npt.mdp, line 70]:
Unknown left-hand 'pull_group0_name' in parameter file
and if i used
pull-coord1-groups = 26 1
26 is the index number of the protein2pull in the in
On 4/4/14, 8:33 AM, Andres Ortega Guerrero wrote:
I'm sorry Justin, My mistake,
when i use this pull code, using grompp, with this pull code
; Pull code
pull= umbrella
pull_geometry = direction ;
;pull_vec1 = 0.0 0.0 1.0 ;
pull_coord1_vec = 0.0 0.0 1.0 ;
;pull_di
On 4/4/14, 8:47 AM, Ahmet yıldırım wrote:
Hi,
The bond types are set properly in ffbonded.itp. But I get the following
errors after grompp command. How can I fix it?
ERROR 1 [file protein_Ion_chain_A2.itp, line 33]:
No default Bond types
ERROR 2 [file protein_Ion_chain_A2.itp, line 34]:
Hi,
The bond types are set properly in ffbonded.itp. But I get the following
errors after grompp command. How can I fix it?
ERROR 1 [file protein_Ion_chain_A2.itp, line 33]:
No default Bond types
ERROR 2 [file protein_Ion_chain_A2.itp, line 34]:
No default Bond types
protein_Ion_chain_A2.it
I'm sorry Justin, My mistake,
when i use this pull code, using grompp, with this pull code
; Pull code
pull= umbrella
pull_geometry = direction ;
;pull_vec1 = 0.0 0.0 1.0 ;
pull_coord1_vec = 0.0 0.0 1.0 ;
;pull_dim= N N Y
pull_start = yes ; def
On 4/4/14, 4:46 AM, Sanchaita wrote:
Hi, I am trying to perform the simulations of a particular protein having
NADH as a cofactor. However, when I try to run pdb2gmx command it
shows an error. It seems that the gromos96 43a2 force field has parameters
for NADH but the labeling do not match the
Hi Bipin,
Just went through your post. I also have the similar issue of making 1 D
free energy plots. I tried it with g_sham and got a file which contains the
bin index and 3 more columns. But I want the energies as a function of the
principal component I'm using.
Could you please help me if you
did you look at the documentation for the pull code?
generally you want to be careful interpreting such calculations ... the
parameters for commonly used
protein force fields were fitted to reproduce equilibrium structures ...
even if they were, in principle,
applicable to what's in between (tran
i was wondering about the same question ...
from using antechamber and amb2gmx.pl output in
simulations i concluded that this seems to work, in other
words the R-B dihedrals are in fact used for improper
dihedrals, you can check by looking at your topology
files ... for improper dihedrals the ce
That should be run on the CPU - the decomposition required to do energy
groups on the GPU defeats the point of using the GPU, so it is not
implemented.
Mark
On Apr 4, 2014 11:31 AM, "michael.b" wrote:
>
> thanks for the reply! ...
>
> to be precise i should add that when i say analyze i actually
for a template and instructions for making a polymer residue database based
on opls you also might want to have a look at gmx-ffoplsp
in http://brunsteiner.net/software.html
this worked for gmx-4.0.7 and should still do so,
only you don't need to edit the FF.dat file anymore but just insert a f
That I do not know.
2014-04-04 11:25 GMT+02:00 michael.b :
>
> thanks for the reply! ...
>
> to be precise i should add that when i say analyze i actually
> mean rerun 4.5.6 trajectories with mdrun-5.0-breta ...
>
> cheers
> michael
>
>
>
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thanks for the reply! ...
to be precise i should add that when i say analyze i actually
mean rerun 4.5.6 trajectories with mdrun-5.0-breta ...
cheers
michael
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Hi,
I am trying to run a simulation of PEO opls-AA with gromacs but significant
information about dihedral angles are missing. Can you direct me to the
paper with PEO opla-aa that you mention in your post.
Thanks in andvance
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Hi, I am trying to perform the simulations of a particular protein having
NADH as a cofactor. However, when I try to run pdb2gmx command it
shows an error. It seems that the gromos96 43a2 force field has parameters
for NADH but the labeling do not match the labeling done in the pdb file.
What
On Apr 4, 2014 9:42 AM, "michael.b" wrote:
>
>
> two questions:
>
> 1) searching this list if found this comment:
> "NOTE: With GPUs, reporting energy group contributions is not supported"
>
> this was true for version 4.6.1
> is it still the case for 4.6.5 and/or for 5.0-beta?
Yes, I think so.
Hello,
I can maybe give you answer on second question. I have used analyzes tool
gmx gangle from 5.0-beta to analyzes trajectories from 4.6.5 and it was OK
for me.
Cheers,
Josip
2014-04-04 9:35 GMT+02:00 michael.b :
>
> two questions:
>
> 1) searching this list if found this comment:
> "NOTE:
Thank you very much for the clarification.
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two questions:
1) searching this list if found this comment:
"NOTE: With GPUs, reporting energy group contributions is not supported"
this was true for version 4.6.1
is it still the case for 4.6.5 and/or for 5.0-beta?
2) if i use mdrun-5.0-beta to analzye trajectories produced with 4.6.5
do i h
You've discarded the legend in the header of the file...
Mark
On Apr 4, 2014 8:17 AM, "richa" wrote:
> Hi all,
>
> I wanted to know, if we can plot one dimensional free energy surfaces along
> the dihedral angles (or any other variable) of alanine di peptide using
> g_sham utility of gromacs.
>
Running mdrun and anything else sharing the same hardware requires explicit
management so that they do not actually share CPU cores. mdrun is designed
to saturate the cores, and dramatic nonlinear degradation is exactly what
should be expected from sharing any core.
But rather than speculate, how
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