Dear Szilard,
Thanks for your message. Your help is priceless and helps advance science more
than many publications. I extend that to many experts who kindly and promptly
answer questions in the mailing list. I wish that could be valued when
evaluating a CV. Sorry for the digression...
The visua
Dear All,
Is there any way to print parameters used for system (just for the
atomtypes present in system). I have all necessary files (top, tpr, gro and
oplsa.ff)
regards,
Jiom
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* Please search
Grep?
On Jun 18, 2013 10:23 AM, "gromacs query" wrote:
> Dear All,
>
> Is there any way to print parameters used for system (just for the
> atomtypes present in system). I have all necessary files (top, tpr, gro and
> oplsa.ff)
>
> regards,
> Jiom
> --
> gmx-users mailing listgmx-users@gromac
GROMACS is not yet magic. You used an atom type not found in your force
field. Over to you. :-)
Mark
On Jun 18, 2013 5:23 AM, "Hasni Arsad" wrote:
> Hi,
>
> I got this error massage when execute this command- grompp -f em.mdp -c
> solvated.pdb -p topol.top
>
>
>
> Program grompp, VERSION 4.6.2
>
Dear Mark,
>> Grep?
Sorry but I mean to say I have say .itp file like this
[ bonds ]
; ai ajfunctc0c1c2c3
1 21
and so on
[ angles ]
; ai aj akfunctc0c1c2c3
2 1 31
and so on.
So I want to extract p
Hi,
I just recently learned from the mailing list that there is an -pp option
in grompp, which should write all parameters into a single top file. Haven't
tried it yet, but it should work.
/Flo
---
Dr. rer. nat. Florian Dommert
Institut für Computerphysik
Universität Stuttgart
Allmandring
Please keep GROMACS usage questions on the gmx-users mailing list. Nobody
here is a private tutor :-)
The error messages you are getting are self-explanatory. You need to think
about why they are arising. Perhaps do some tutorials to get a feel for
normal workflows, and how best to modify them to
Dear Florian,
I used -pp as you suggested but it dumps every thing from oplsaa (this is
FF I am using). So may be I think this gives an output which can be used as
an independent file, as it includes everything, instead of directing to
oplsaa.ff directory.
But still am not getting to print params
What should i do with this error massage:
Program grompp, VERSION 4.6.2
Source code file:
/home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563
Fatal error:
number of coordinates in coordinate file (solv.gro, 50853)
does not match topology (topol.top, 50816)
For more
grompp does this kind of parsing and pruning while producing the .tpr file,
and the result can be dumped with gmxdump. Each interaction type that is
used is listed and the sets of parameters are also listed and the
cross-reference is made. But it is not really intended for human digestion.
You have
On 6/17/13 4:58 PM, Hyunjin Kim wrote:
Hi,
I sent the following email last Saturday and I haven't got any reply yet.
I wonder whether you can suggest something regarding this issue.
Thanks in advance.
**
I
Dear Mark,
>> You haven't stated your purpose for the information, so it's hard to be
helpful.
I have two structures in one file. One is using original OPLSAA ("A") and
other using modified OPLSAA ("B"). While grompping I get over riding params
which is OK unless "A" and "B" has same angle/dihedr
gmxcheck will compare .tpr files?
On Tue, Jun 18, 2013 at 12:09 PM, gromacs query wrote:
> Dear Mark,
>
> >> You haven't stated your purpose for the information, so it's hard to be
> helpful.
>
> I have two structures in one file. One is using original OPLSAA ("A") and
> other using modified OPL
I'm trying to compare the hydrophobic surface generated from my trajectory
with g_sas to a range of random coil .pdb files with my protein sequence,
but I can't figure out how to make the structure+mass input that is required
for g_sas from my pdb files i.e. in the manual
"Structure+mass(db): tpr t
On 6/18/13 7:41 AM, erin.cutts wrote:
I'm trying to compare the hydrophobic surface generated from my trajectory
with g_sas to a range of random coil .pdb files with my protein sequence,
but I can't figure out how to make the structure+mass input that is required
for g_sas from my pdb files i.e
it sends back a fatal error if you don't put in a tp file.
I'm more than happy to send in a tpr file, I just need to figure out how to
generate it.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/g-sas-on-pdb-files-tp5009248p5009250.html
Sent from the GROMACS Users Forum mail
On 6/18/13 8:22 AM, erin.cutts wrote:
it sends back a fatal error if you don't put in a tp file.
I'm more than happy to send in a tpr file, I just need to figure out how to
generate it.
Refer to any tutorial. A .tpr file is a run input file that Gromacs uses for a
simulation.
-Justin
--
Hello,
I am a new user to vmd and I wanted to know how to generate dcd files.
Reading from posts that already exist here about dcd file generation, I
found out that we can use wordom to do this generation which when I tried to
configure in linux, didn't work. I got some help thinking this was my
Hello,
I am a new user to vmd and I wanted to know how to generate dcd files.
Reading from posts that already exist here about dcd file generation, I
found out that we can use wordom to do this generation which when I tried to
configure in linux, didn't work. I got some help thinking this was my
2013/6/18 Hasni Arsad
> What should i do with this error massage:
>
Google it.
> Program grompp, VERSION 4.6.2
> Source code file:
> /home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563
>
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 50853)
>
Hi,
I want to use thermodynamic integration for calculating free energy of binding
of ligand to its receptor protein. For that I would like to follow the two step
approach: first decoupling Coulombic and then vdW interactions.
1. Shall I start with the same coordinate and topology files for bot
On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul wrote:
>
>
> On 6/10/13 5:16 AM, Steven Neumann wrote:
>
>> Thank you.
>> Do you know whether it is possible to use the 5th order polynomial for
>> angles in Gromacs? I know I can use tables but wish to fit my data into
>> such a function.
>>
>>
> No
Dear GROMACS user,
I have been trying to define parameters for virtual sites in CHARMM lipid,
and I would like to know if there is something simillar to the [ bondtypes ]
for virtual sites.
Specifically the way I specify the parameters now is by having lines in the
topology such as (for a 3fout vi
On 6/18/13 11:39 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul wrote:
On 6/10/13 5:16 AM, Steven Neumann wrote:
Thank you.
Do you know whether it is possible to use the 5th order polynomial for
angles in Gromacs? I know I can use tables but wish to fit my data
On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann wrote:
> On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul wrote:
>
> >
> >
> > On 6/10/13 5:16 AM, Steven Neumann wrote:
> >
> >> Thank you.
> >> Do you know whether it is possible to use the 5th order polynomial for
> >> angles in Gromacs? I know I c
On 6/18/13 12:20 PM, Bastien Loubet wrote:
Dear GROMACS user,
I have been trying to define parameters for virtual sites in CHARMM lipid,
and I would like to know if there is something simillar to the [ bondtypes ]
for virtual sites.
Specifically the way I specify the parameters now is by havin
Hi Tsjerk,
I really appreciate your comments. I proceeded as you recommended, and
calculate the subspace overlap in the way you proposed.
I first performed the analysis varying the starting points, instead of the
end ones. I start from 110 ns down to 0ns, with 10ns time intervals:
Normalized DT
Hi everybody!
I am trying to simulate a lipid membrane at zero pressure and at a range of
temperatures. I am using a bilayer from the Martini website. I was having a
problem with the Parinello-Rahman barostat so I switched to Berendsen and am
also keeping the height of the box constant otherwise i
Hi everybody,
It seems that my runs still are crashing. I even decided not to switch over
to Parinello-Rahman and continue doing the simulation with a Berendsen
barostat and it shuts off after a period of time. I am extremely puzzled as
to why this is happening especially since Berendsen is pretty
On 6/18/13 3:13 PM, Neha wrote:
Hi everybody!
I am trying to simulate a lipid membrane at zero pressure and at a range of
temperatures. I am using a bilayer from the Martini website. I was having a
problem with the Parinello-Rahman barostat so I switched to Berendsen and am
also keeping the he
Dear,
In the MD, I find that when the ligand keep in the active site , the
channel formed by two loops is closed. without the ligand the channel is
opened. I don't know how to describe the change of channel. could i describe
the channel by calculating the the most narrow distance(mass ce
Hi,
Well, I tried running a simulation at ref_p to 1.0 and got the same error as
earlier, so it doesn't seem to be that. That was the only thing I changed in
the mdp file, so I am still not sure as to where the problem is.
Justin Lemkul wrote
> On 6/18/13 3:13 PM, Neha wrote:
>> Hi everybody!
>>
Do you mean the commands of inflateGRO controls the deletion radius?
The command which I use is what I got from tutorial:
#perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat
Am I supposed to decrease 5 as deletion radius?
Would you please give me a hint to go on?
Thanks fo
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