On 19/09/2012 4:37 PM, Tsjerk Wassenaar wrote:
g_bond.c / gmx_bond.c ?
No, I checked earlier and it uses index groups. trjconv -pbc whole is no
good either.
Mark
Cheers,
Tsjerk
On Sep 18, 2012 9:50 PM, "Mark Abraham" wrote:
On 19/09/2012 12:49 PM, Amit Shavit wrote: > > Hello, > > I'm
g_bond.c / gmx_bond.c ?
Cheers,
Tsjerk
On Sep 18, 2012 9:50 PM, "Mark Abraham" wrote:
On 19/09/2012 12:49 PM, Amit Shavit wrote: > > Hello, > > I'm relatively
new to GROMACS, and I need ...
The easiest way to learn how to use the information in the .tpr is to work
by analogy from an existing t
On 19/09/2012 12:49 PM, Amit Shavit wrote:
Hello,
I'm relatively new to GROMACS, and I need to write some of my own analysis
tools using the template.c file.
I have been able to figure out most of the structure of it, and how the C
Structs are used. That is to say, I can successfully retrieve pa
I forgot to mention that the bond info should be in the .tpr file somewhere
as it was processed from the topology and I think gmxdump will also show
the connectivities.
On 2012-09-18 10:49:25PM -0400, Amit Shavit wrote:
> Hello,
>
> I'm relatively new to GROMACS, and I need to write some of my ow
The topol.top/.itp files have the pairwise bond information.
On 2012-09-18 10:49:25PM -0400, Amit Shavit wrote:
> Hello,
>
> I'm relatively new to GROMACS, and I need to write some of my own analysis
> tools using the template.c file.
> I have been able to figure out most of the structure of it,
Hello,
I'm relatively new to GROMACS, and I need to write some of my own analysis
tools using the template.c file.
I have been able to figure out most of the structure of it, and how the C
Structs are used. That is to say, I can successfully retrieve particle
positions, residue IDs, residue names,
Dear all,
I have been reading about PRODRG that takes a PDB file as an input and produces
topologies compatible with GROMACS as an output. Can this program be then
considered as a solution to the problem of missing residues in GROMACS like
LIG?
N.B: I am using the OPLSAA force field .I also
Hi Justin
I really forgot this old mail. I am sorry for that.
editconf worked :)
Greetings
Lara
- Ursprüngliche Message -
Von: Justin Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 16:04 Dienstag, 18.September 2012
Betreff: Re: [gmx-users] PDB and XYZ S
Hi Gmx Community,
I am doing Glutamate to Alanine mutation in presence and absence of a
ligand.
The Coulomb transformation is yielding the following results:
Glu--->Ala + ligand = 790.109 kJ/mol
Glu--->Ala + no ligand = 787.33 kJ/mol
During the LJ transformation
Glu--->Ala + ligand = - 24.87 kJ/m
As mentioned, you should make RESP charges for AMBER parameters. ESP parameters
are furthermore often a bit bizarre (aliphatic carbons with charge well below
-1etc.).
Erik
14.11 skrev tarak karmakar:
> Thanks Mark.
>
> I have gone through the link "Parameterization of novel molecules" and
> I
On 9/18/12 1:56 PM, Ali Alizadeh wrote:
Dear Justin
Your link did not help me for generate the methane.itp file but generated
my propane.itp file.
I would suggest you contact the developers of SwissParam to understand why it
did not work. Likely there are some limitations on what types of
On 9/18/12 12:42 PM, SIMONE BROGI wrote:
Dear gromacs user,
I have a complex generated by docking calculation and I would perform a MD
by gromacs. I have a problem with ligand atoms. In the pdb file the ligand
appears as UNK and if I process this file in order to start simulation I
receive this
Dear gromacs user,
I have a complex generated by docking calculation and I would perform a MD
by gromacs. I have a problem with ligand atoms. In the pdb file the ligand
appears as UNK and if I process this file in order to start simulation I
receive this messagge error:
"Residue 'UNK' not found in
Dear Justin
Thank you so much,
Sincerely
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the li
On 9/18/12 10:25 AM, Ali Alizadeh wrote:
Dear All users
How to generate a .itp file for molecules?(for example, CHARMM ff and
alkanes.)
http://swissparam.ch/
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia
What you are talking about with conducting only 2 end-state simulations sounds
like "free energy perturbation" and
it relies on conformational overlap of the two endstates. I don't think that it
is going to give correct free energies
here. The reason to do umbrella sampling (US) is to ensure that
On 9/18/12 9:58 AM, Lara Bunte wrote:
Hello
Is it possible with GROMACS to convert a given .pdb structure file to a .xyz
structure file?
http://gromacs.5086.n6.nabble.com/pdb-to-xyz-file-format-td4998284.html
-Justin
--
Justin A. Lemkul, Ph.D.
Re
Hello
Is it possible with GROMACS to convert a given .pdb structure file to a .xyz
structure file?
Thanks for help
Greetings
Lara
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Suppo
Dear All,
Ill give this a shot. I guess it depends on your entire system (ie protein
+DNA or just DNA) and what it is you waant to observe.
and example of why answereing becomes complex. if A) I want to just look at
say the total delta G,S or H. I would only need to EQ several starting
stru
Hi Sara,
NPT also requires a routine for temperature coupling. What makes you wonder
about the suitability of v-rescale for that? If you check the mdp files
from tutorial stuff, you'll probably encounter the v-rescale method used in
the NpT simulations.
Cheers,
Tsjerk
On Sep 18, 2012 7:12 AM, "
On 18/09/2012 11:21 PM, Bharath K. Srikanth wrote:
Hi all
While attempting to simulate the self assembly of a course-grained DSPC
lipids, I ran into a problem using the genbox command.
I first used genbox to create a box of 32 DSPC lipids, of dimensions 20 x
20 x 20 nm^3. The command used was
On 9/18/12 9:21 AM, Bharath K. Srikanth wrote:
Hi all
While attempting to simulate the self assembly of a course-grained DSPC
lipids, I ran into a problem using the genbox command.
I first used genbox to create a box of 32 DSPC lipids, of dimensions 20 x
20 x 20 nm^3. The command used was
ge
Hi all
While attempting to simulate the self assembly of a course-grained DSPC
lipids, I ran into a problem using the genbox command.
I first used genbox to create a box of 32 DSPC lipids, of dimensions 20 x
20 x 20 nm^3. The command used was
genbox -ci dspc_single.gro -nmol 32 -box 20 20 20 -tr
Please don't reply to the entire digest.
On 9/18/12 9:09 AM, Praveen Kumar Sappidi wrote:
Dr Justin
This is my Topolofy file for Ethanol
[ moleculetype ]
; Namenrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB
Dear Gromacs Users,
I have doubt about temperature bath coupling (v-rescale). I use this method
(v-rescale) for my system, and my system is NPT ensemble.
Has it problem? is v-rescale just used for NVT ensemble or it doesn't have
restriction?
Please help me.
Thank you in advance
Best Regards
Sar
Dr Justin
This is my Topolofy file for Ethanol
[ moleculetype ]
; Namenrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 H 1 ETHH EH 1 0.408 1.008 ; qtot
0.
On 9/18/12 8:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Okey,
now I tried it without any fixed residues. But still the energy after the
minimization is not very low and I still get the LINCS warnings.
The mdp file I use for the minimization looks like this:
define
On Tue, Sep 18, 2012 at 2:43 PM, Justin Lemkul wrote:
>
>
> On 9/18/12 8:29 AM, Dr. Vitaly Chaban wrote:
>>
>> Dear All -
>>
>> I an using the current version of gromacs. Although I have
>>
>> nstxout = 0
>> nstvout = 0
>> nstfout = 0
>>
>> in the
On 9/18/12 8:56 AM, Praveen Kumar Sappidi wrote:
Hi Justin
prompt for calculation i have shown below
Reading file eth-water60%-production.tpr, VERSION 4.0.7 (single precision)
Note: tpx file_version 58, software version 73
Specify 2 groups to analyze:
Group 0 ( System) has 19412
Okey,
now I tried it without any fixed residues. But still the energy after the
minimization is not very low and I still get the LINCS warnings.
The mdp file I use for the minimization looks like this:
define = -DPOSRES
integrator = steep
emtol = 1
On 9/18/12 8:29 AM, Dr. Vitaly Chaban wrote:
Dear All -
I an using the current version of gromacs. Although I have
nstxout = 0
nstvout = 0
nstfout = 0
in the MDP file, the traj.trr file appears during the MD run (and is
quite large). In olde
On 9/18/12 8:08 AM, Praveen Kumar Sappidi wrote:
Hi all
Am Simulating Ethanol-water system using Gromacs4.0.7
the problem is am not able to calculate number of hydrogen bonds in ethanol
and water-ethanol.
i can see a small peak at 0.24 of Ethanol-water RDFs and visually also i can
see hyd
Dear All -
I an using the current version of gromacs. Although I have
nstxout = 0
nstvout = 0
nstfout = 0
in the MDP file, the traj.trr file appears during the MD run (and is
quite large). In older versions, there was no traj.trr with such an
in
Thanks Mark.
I have gone through the link "Parameterization of novel molecules" and
I see quantum calculations can be handy for this type of charge
calculation (AMBER). So for the unprotonated tyrosine, I am taking two
more amino acids (left and right) and calculating ESP charges of the
tri-peptid
Hi all
Am Simulating Ethanol-water system using Gromacs4.0.7
the problem is am not able to calculate number of hydrogen bonds in ethanol
and water-ethanol.
i can see a small peak at 0.24 of Ethanol-water RDFs and visually also i can
see hydrogen bonding is formed
am using command g_hbond -f *
On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
I need the rest of the structure just as it is now because I want to do
electrostatic analysis with it.
Another thing worth considering - why do you necessarily need the rest of the
structure to be identical? Or perhaps
Looks like there is still something clashing with atom 979.
The resulting force after EM was close to 1, which is not very much
minimized at all...
What is atom 979 and what is near it?
On 2012-09-18 01:22:25PM +0200, reising...@rostlab.informatik.tu-muenchen.de
wrote:
> I need the rest of t
On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
I need the rest of the structure just as it is now because I want to do
electrostatic analysis with it.
I just added the phosphate manually and so I want to minimize and run a
short MD with it.
I added the dihedraltype of
I need the rest of the structure just as it is now because I want to do
electrostatic analysis with it.
I just added the phosphate manually and so I want to minimize and run a
short MD with it.
I added the dihedraltype of the amber database
(http://personalpages.manchester.ac.uk/staff/Richard.Bryc
Thank you very much for your answer.
I managed it now to get the right index groups.
> The selections are boolean (like a search).
>
> So to include both 6 and 7 you would use 6 | 7 (make the selection of 6 or
> 7)
>
> so you probably want something like ! res65 | ! res 6 etc.
>
>
> On 2012-09-18
The selections are boolean (like a search).
So to include both 6 and 7 you would use 6 | 7 (make the selection of 6 or 7)
so you probably want something like ! res65 | ! res 6 etc.
On 2012-09-18 10:56:14AM +0200, reising...@rostlab.informatik.tu-muenchen.de
wrote:
> Hi everybody,
> I want to
Hi everybody,
I want to make two index groups for my protein. The first one should
contain the whole protein except of the residues :
TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80
I tried it with the arguments:
"protein" &! res 65 &! res 6 &! res 7 &! res 61 &! res 64 &! res 80
"protein" &! res 65 6 7 6
42 matches
Mail list logo
