date:20150911

[gmx-users] How to create a spherocylindrical wall

2015-09-11 Thread Jagannath Mondal

Hi
  I would like to perform a simulation ( without any periodic boundary
condition) where I need to have a wall of spherocylindrical geometry. In
other words the particles will be confined inside a spherocylinder.

 Is there any good suggestion on how to achieve that in gromacs?

1) One option I thought of achieving that is by having a spherocylindrical
wall potential.  Is there a way of putting the wall potential in the form
of a table-potential ? (Not sure cylinder option in gromacs umbrella
sampling  not going to be helpful).

2)  Or,should I put a bunch of hard sphere which constitute the
spherocylindrical boundary so that the particles inside the spherocylinder
will have a repulsive interaction each time they come towards the boundary ?

Thanks
Jagannath
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[gmx-users] g_hbond

2015-09-11 Thread Shahid Nayeem

Dear all
I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file.
Then with xpm2ps I converted .xpm to .eps file. I get half the number of
rows in .eps file as compared to .ndx file. when using Justins perl script
I got summary of existence file and here 12 bonds are shown but in .eps
file only 6 rows are plotted. I know that the bonds are plotted in reverse
order but here only half number of bonds are plotted in .eps file. please
help to resolve this issue.
shahid
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Re: [gmx-users] gromacs-5.1 with charmm36.ff

2015-09-11 Thread Krzysztof Kuczera


Thanks for the quick response
- that fixed my problem
Krzysztof

On 9/10/15 5:36 PM, Justin Lemkul wrote:



On 9/10/15 6:17 PM, Krzysztof Kuczera wrote:

Hi
I have run into a strange problem when making an urea+tip3p water box
When trying to set up an energy minimization with gromacs-5.1  I get 
a grompp

error:

Program gmx grompp, VERSION 5.1
Source code file:
/home/kuczera/prog/gromacs-5.1/src/gromacs/gmxpreprocess/toppush.c, 
line: 908


Fatal error:
Unknown bond_atomtype cn9

Here is the strangeness:

- grompp and mdrun work OK with version 5.0.4
- I am using the same force field since winter - from 
charmm36-nov2014.ff.tar,

which I add
manually to the successive 5.x directories as I upgrade the 
GROMACS versions
- my system only has UREA and TIP3P, which do not contain atom names 
or types = CN9
looking in the CHARMM36 merged.rtp file shows that CN9 atoms are 
in nucleic

acids



Please get the latest version of the force field from our website.  
There have been changes related to case sensitivity in the code, and I 
have updated the force field files accordingly.


http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

-Justin




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The University of Kansas
1251 Wescoe Hall Drive, 5090 Malott Hall
Lawrence, KS 66045
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Re: [gmx-users] Cyclic peptide by using specbond.dat

2015-09-11 Thread João M . Damas

This does not seem related with specbond.dat, but rather a problem with the
chains: each residue is a different chain and maybe that is causing
troubles with the termini. Remove the chain ID or make them all chain A.

João

On Fri, Sep 11, 2015 at 6:39 PM, Nikhil Maroli  wrote:

> *Dear Gromacs users*
> *i have been having a bit of issues generating accurate topology for cyclic
> peptide*
>
> *i added extra terms in specbond.dat (Last Line)*
> *as *
>
> 9
>
> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
>
> CYS SG 1 HEM FE 2 0.25 CYS2 HEME
>
> CYS SG 1 HEM CAB 1 0.18 CYS2 HEME
>
> CYS SG 1 HEM CAC 1 0.18 CYS2 HEME
>
> HIS NE2 1 HEM FE 1 0.2 HIS1 HEME
>
> MET SD 1 HEM FE 1 0.24 MET HEME
>
> CO  C   1   HEMEFE  1   0.19CO  HEME
> CYM SG  1   CYM SG  1   0.2 CYS2CYS2
>
> *LYS C 1 ALA N 1 0.135 LYS ALA*
>
>
> and my pdb file is as
> SEQRES   1 A4  ALA LEU GLN LYS
> LINK N   ALA A   1 C   LYS A   4
>  1.34
> ATOM  1  N   ALA A   1  -7.317  -0.819   1.765  1.00  0.00
>   N
> ATOM  2  H   ALA A   1  -6.725  -1.565   2.103  1.00  0.00
>   H
> ATOM  3  CA  ALA A   1  -6.768   0.542   1.865  1.00  0.00
>   C
> ATOM  4  HA  ALA A   1  -7.224   1.212   1.142  1.00  0.00
>   H
> ATOM  5  C   ALA A   1  -5.244   0.544   1.585  1.00  0.00
>   C
> ATOM  6  O   ALA A   1  -4.449   0.351   2.495  1.00  0.00
>   O
> ATOM  7  CB  ALA A   1  -7.092   1.097   3.262  1.00  0.00
>   C
> ATOM  8 HB1  ALA A   1  -6.673   0.442   4.029  1.00  0.00
>   H
> ATOM  9 HB1  ALA A   1  -8.168   1.171   3.407  1.00  0.00
>   H
> ATOM 10 HB1  ALA A   1  -6.651   2.089   3.375  1.00  0.00
>   H
> ATOM 11  N   LEU B   2  -4.781   0.766   0.348  1.00  0.00
>   N
> ATOM 12  H   LEU B   2  -3.776   0.718   0.265  1.00  0.00
>   H
> ATOM 13  CA  LEU B   2  -5.549   0.859  -0.902  1.00  0.00
>   C
> ATOM 14  HA  LEU B   2  -6.305   1.635  -0.790  1.00  0.00
>   H
> ATOM 15  C   LEU B   2  -6.247  -0.477  -1.208  1.00  0.00
>   C
> ATOM 16  O   LEU B   2  -5.673  -1.538  -0.993  1.00  0.00
>   O
> ATOM 17  CB  LEU B   2  -4.589   1.279  -2.034  1.00  0.00
>   C
> ATOM 18 HB1  LEU B   2  -4.111   2.220  -1.754  1.00  0.00
>   H
> ATOM 19 HB1  LEU B   2  -3.807   0.520  -2.117  1.00  0.00
>   H
> ATOM 20  CG  LEU B   2  -5.238   1.454  -3.426  1.00  0.00
>   C
> ATOM 21  HG  LEU B   2  -5.676   0.505  -3.738  1.00  0.00
>   H
> ATOM 22  CD1 LEU B   2  -6.340   2.525  -3.427  1.00  0.00
>   C
> ATOM 23 HD11 LEU B   2  -6.723   2.656  -4.440  1.00  0.00
>   H
> ATOM 24 HD12 LEU B   2  -5.940   3.476  -3.074  1.00  0.00
>   H
> ATOM 25 HD13 LEU B   2  -7.169   2.224  -2.789  1.00  0.00
>   H
> ATOM 26  CD2 LEU B   2  -4.160   1.833  -4.450  1.00  0.00
>   C
> ATOM 27 HD21 LEU B   2  -4.605   1.920  -5.442  1.00  0.00
>   H
> ATOM 28 HD22 LEU B   2  -3.391   1.060  -4.482  1.00  0.00
>   H
> ATOM 29 HD23 LEU B   2  -3.700   2.785  -4.180  1.00  0.00
>   H
> ATOM 30  N   GLN C   3  -7.497  -0.424  -1.671  1.00  0.00
>   N
> ATOM 31  H   GLN C   3  -7.910   0.469  -1.882  1.00  0.00
>   H
> ATOM 32  CA  GLN C   3  -8.323  -1.613  -1.897  1.00  0.00
>   C
> ATOM 33  HA  GLN C   3  -8.020  -2.397  -1.198  1.00  0.00
>   H
> ATOM 34  C   GLN C   3  -9.820  -1.324  -1.624  1.00  0.00
>   C
> ATOM 35  O   GLN C   3 -10.666  -1.591  -2.471  1.00  0.00
>   O
> ATOM 36  CB  GLN C   3  -8.045  -2.130  -3.325  1.00  0.00
>   C
> ATOM 37 HB1  GLN C   3  -8.470  -1.427  -4.044  1.00  0.00
>   H
> ATOM 38 HB2  GLN C   3  -6.967  -2.154  -3.497  1.00  0.00
>   H
> ATOM 39  CG  GLN C   3  -8.587  -3.552  -3.580  1.00  0.00
>   C
> ATOM 40 HG1  GLN C   3  -7.751  -4.250  -3.637  1.00  0.00
>   H
> ATOM 41 HG1  GLN C   3  -9.225  -3.868  -2.754  1.00  0.00
>   H
> ATOM 42  CD  GLN C   3  -9.400  -3.641  -4.869  1.00  0.00
>   C
> ATOM 43  OE1 GLN C   3  -8.993  -4.228  -5.857  1.00  0.00
>   O
> ATOM 44  NE2 GLN C   3 -10.567  -3.038  -4.913  1.00  0.00
>   N
> ATOM 45 HE21 GLN C   3 -11.082  -3.101  -5.769  1.00  0.00
>   H
> ATOM 46 HE22 GLN C   3 -10.883  -2.515  -4.103  1.00  0.00
>   H
> ATOM 47  N   LYS D   4 -10.243  -0.726  -0.500  1.00  0.00
>   N
> ATOM 48  H   LYS D   4 -11.247  -0.617  -0.471  1.00  0.00
>   H
> ATOM 49  CA  LYS D   4  -9.503  -0.233   0.679  1.00  0.00
>   C
> ATOM 50  HA  LYS D   4  -8.973   0.661   0.371  1.00  0.00
>   H
> ATOM 51  C   LYS D   4  -8.483  -1.241   1.259  1.00  0.00
>   C
> ATOM 52  O   LYS D   4  -8.735  -2.437   1.259  1.00  0.00
>   O
> ATOM 53  CB  LYS D   4 -10.517   0.166   1.774  1.00  0.00
>   C
> ATOM

Re: [gmx-users] Cyclic peptide by using specbond.dat

2015-09-11 Thread Mark Abraham

Hi,

Yes, that's exactly what parts of the output are saying.

Mark

On Fri, 11 Sep 2015 22:45 João M. Damas  wrote:

> This does not seem related with specbond.dat, but rather a problem with the
> chains: each residue is a different chain and maybe that is causing
> troubles with the termini. Remove the chain ID or make them all chain A.
>
> João
>
> On Fri, Sep 11, 2015 at 6:39 PM, Nikhil Maroli 
> wrote:
>
> > *Dear Gromacs users*
> > *i have been having a bit of issues generating accurate topology for
> cyclic
> > peptide*
> >
> > *i added extra terms in specbond.dat (Last Line)*
> > *as *
> >
> > 9
> >
> > CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
> >
> > CYS SG 1 HEM FE 2 0.25 CYS2 HEME
> >
> > CYS SG 1 HEM CAB 1 0.18 CYS2 HEME
> >
> > CYS SG 1 HEM CAC 1 0.18 CYS2 HEME
> >
> > HIS NE2 1 HEM FE 1 0.2 HIS1 HEME
> >
> > MET SD 1 HEM FE 1 0.24 MET HEME
> >
> > CO  C   1   HEMEFE  1   0.19CO  HEME
> > CYM SG  1   CYM SG  1   0.2 CYS2CYS2
> >
> > *LYS C 1 ALA N 1 0.135 LYS ALA*
> >
> >
> > and my pdb file is as
> > SEQRES   1 A4  ALA LEU GLN LYS
> > LINK N   ALA A   1 C   LYS A   4
> >  1.34
> > ATOM  1  N   ALA A   1  -7.317  -0.819   1.765  1.00  0.00
> >   N
> > ATOM  2  H   ALA A   1  -6.725  -1.565   2.103  1.00  0.00
> >   H
> > ATOM  3  CA  ALA A   1  -6.768   0.542   1.865  1.00  0.00
> >   C
> > ATOM  4  HA  ALA A   1  -7.224   1.212   1.142  1.00  0.00
> >   H
> > ATOM  5  C   ALA A   1  -5.244   0.544   1.585  1.00  0.00
> >   C
> > ATOM  6  O   ALA A   1  -4.449   0.351   2.495  1.00  0.00
> >   O
> > ATOM  7  CB  ALA A   1  -7.092   1.097   3.262  1.00  0.00
> >   C
> > ATOM  8 HB1  ALA A   1  -6.673   0.442   4.029  1.00  0.00
> >   H
> > ATOM  9 HB1  ALA A   1  -8.168   1.171   3.407  1.00  0.00
> >   H
> > ATOM 10 HB1  ALA A   1  -6.651   2.089   3.375  1.00  0.00
> >   H
> > ATOM 11  N   LEU B   2  -4.781   0.766   0.348  1.00  0.00
> >   N
> > ATOM 12  H   LEU B   2  -3.776   0.718   0.265  1.00  0.00
> >   H
> > ATOM 13  CA  LEU B   2  -5.549   0.859  -0.902  1.00  0.00
> >   C
> > ATOM 14  HA  LEU B   2  -6.305   1.635  -0.790  1.00  0.00
> >   H
> > ATOM 15  C   LEU B   2  -6.247  -0.477  -1.208  1.00  0.00
> >   C
> > ATOM 16  O   LEU B   2  -5.673  -1.538  -0.993  1.00  0.00
> >   O
> > ATOM 17  CB  LEU B   2  -4.589   1.279  -2.034  1.00  0.00
> >   C
> > ATOM 18 HB1  LEU B   2  -4.111   2.220  -1.754  1.00  0.00
> >   H
> > ATOM 19 HB1  LEU B   2  -3.807   0.520  -2.117  1.00  0.00
> >   H
> > ATOM 20  CG  LEU B   2  -5.238   1.454  -3.426  1.00  0.00
> >   C
> > ATOM 21  HG  LEU B   2  -5.676   0.505  -3.738  1.00  0.00
> >   H
> > ATOM 22  CD1 LEU B   2  -6.340   2.525  -3.427  1.00  0.00
> >   C
> > ATOM 23 HD11 LEU B   2  -6.723   2.656  -4.440  1.00  0.00
> >   H
> > ATOM 24 HD12 LEU B   2  -5.940   3.476  -3.074  1.00  0.00
> >   H
> > ATOM 25 HD13 LEU B   2  -7.169   2.224  -2.789  1.00  0.00
> >   H
> > ATOM 26  CD2 LEU B   2  -4.160   1.833  -4.450  1.00  0.00
> >   C
> > ATOM 27 HD21 LEU B   2  -4.605   1.920  -5.442  1.00  0.00
> >   H
> > ATOM 28 HD22 LEU B   2  -3.391   1.060  -4.482  1.00  0.00
> >   H
> > ATOM 29 HD23 LEU B   2  -3.700   2.785  -4.180  1.00  0.00
> >   H
> > ATOM 30  N   GLN C   3  -7.497  -0.424  -1.671  1.00  0.00
> >   N
> > ATOM 31  H   GLN C   3  -7.910   0.469  -1.882  1.00  0.00
> >   H
> > ATOM 32  CA  GLN C   3  -8.323  -1.613  -1.897  1.00  0.00
> >   C
> > ATOM 33  HA  GLN C   3  -8.020  -2.397  -1.198  1.00  0.00
> >   H
> > ATOM 34  C   GLN C   3  -9.820  -1.324  -1.624  1.00  0.00
> >   C
> > ATOM 35  O   GLN C   3 -10.666  -1.591  -2.471  1.00  0.00
> >   O
> > ATOM 36  CB  GLN C   3  -8.045  -2.130  -3.325  1.00  0.00
> >   C
> > ATOM 37 HB1  GLN C   3  -8.470  -1.427  -4.044  1.00  0.00
> >   H
> > ATOM 38 HB2  GLN C   3  -6.967  -2.154  -3.497  1.00  0.00
> >   H
> > ATOM 39  CG  GLN C   3  -8.587  -3.552  -3.580  1.00  0.00
> >   C
> > ATOM 40 HG1  GLN C   3  -7.751  -4.250  -3.637  1.00  0.00
> >   H
> > ATOM 41 HG1  GLN C   3  -9.225  -3.868  -2.754  1.00  0.00
> >   H
> > ATOM 42  CD  GLN C   3  -9.400  -3.641  -4.869  1.00  0.00
> >   C
> > ATOM 43  OE1 GLN C   3  -8.993  -4.228  -5.857  1.00  0.00
> >   O
> > ATOM 44  NE2 GLN C   3 -10.567  -3.038  -4.913  1.00  0.00
> >   N
> > ATOM 45 HE21 GLN C   3 -11.082  -3.101  -5.769  1.00  0.00
> >   H
> > ATOM 46 HE22 GLN C   3 -10.883  -2.515  -4.103  1.00  0.00
> >   H
> > ATOM 47  N   LYS D   4 -10.243  -0.726  -0.500  1.00  0.00
> >   N
> > ATOM 48  H   LYS D   4 -11.247  -0.617

[gmx-users] Protein-ligand interaction calculation

2015-09-11 Thread michael zhenin

Hello,

I have simulated (REMD simulation) a protein complexed with a ligand and
wanted to know if there is any option for calculating the non bonded
energies between the protein and the ligand (throughout the entire
simulation).

Thanks you in advance,

Michael.
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 137, Issue 61

2015-09-11 Thread Nikhil Maroli

Thanks Mark and Joao
I'm  able to make peptide bond for the Cyclic peptide using specbond.dat
but there is a additional Oxygen and Hydrogen atom on the Carbon and
Nitrogen atom.when i run pdb2gmx selected Amber forcefield  it didnt ask
for the terminals and created topology with amid bond for the cyclic
ring.but when i select the CHARMM forcefield it asking for the terminals
and selected NONE but  it shows the error even after done as you said
before ( Remove the chain ID or make them all chain A. )

*There is a dangling bond at at least one of the terminal ends. Fix
yourcoordinate
file, add a new terminal database entry (.tdb), or select the
 proper existing terminal entry.**For more information and tips for
troubleshooting, please check the GROMACS*

Thanks
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Re: [gmx-users] Protein-ligand interaction calculation

2015-09-11 Thread Justin Lemkul




On 9/11/15 9:46 AM, michael zhenin wrote:

Hello,

I have simulated (REMD simulation) a protein complexed with a ligand and
wanted to know if there is any option for calculating the non bonded
energies between the protein and the ligand (throughout the entire
simulation).



Use energygrps in the .mdp file, regenerate new .tpr, and use mdrun -rerun on 
the existing trajectories.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] g_hbond

2015-09-11 Thread Justin Lemkul




On 9/11/15 2:43 AM, Shahid Nayeem wrote:

Dear all
I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file.
Then with xpm2ps I converted .xpm to .eps file. I get half the number of
rows in .eps file as compared to .ndx file. when using Justins perl script
I got summary of existence file and here 12 bonds are shown but in .eps
file only 6 rows are plotted. I know that the bonds are plotted in reverse
order but here only half number of bonds are plotted in .eps file. please
help to resolve this issue.


You're probably looking at the wrong entry in the index file.  Hard to imagine 
these could be mismatched.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] How to create a spherocylindrical wall

2015-09-11 Thread Barnett, James W

On Fri, 2015-09-11 at 11:57 +0530, Jagannath Mondal wrote:
> Hi
>   I would like to perform a simulation ( without any periodic
> boundary
> condition) where I need to have a wall of spherocylindrical geometry.
> In
> other words the particles will be confined inside a spherocylinder.
> 
>  Is there any good suggestion on how to achieve that in gromacs?
> 
> 1) One option I thought of achieving that is by having a
> spherocylindrical
> wall potential.  Is there a way of putting the wall potential in the
> form
> of a table-potential ? (Not sure cylinder option in gromacs umbrella
> sampling  not going to be helpful).

This might be do-able and would not require a table potential. Check
out flat-bottom restraints in section 4.3.2 in the reference (PDF)
manual.

> 
> 2)  Or,should I put a bunch of hard sphere which constitute the
> spherocylindrical boundary so that the particles inside the
> spherocylinder
> will have a repulsive interaction each time they come towards the
> boundary ?

I'm not sure how you would implement this in a simple way with GROMACS.

-- 
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.ed
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Re: [gmx-users] Creating a box of water with density 1000 g/l

2015-09-11 Thread Justin Lemkul




On 9/11/15 11:46 AM, Ebert Maximilian wrote:

Thanks for the reply. I think I can simulate it now. The only thing I don’t 
understand and this is in reference to my other post: OPLS/AA parameters for 
2-propanol
How can the self-diffusion coefficient be a good measure for testing my 
parameters if for TIP3P water the self-diffusion coefficient ist 6 x 10^-9 m2 
s-1 but the experimental value is around 2.3 x 10^-9 m2 s-1. So if even for a 
highly used water model the coefficient doesn’t fit how can I make any 
assumption about the quality of my parameters for 2-propanol?



Just because one molecule has flawed parameters doesn't mean you shouldn't 
consider this as viable target data for other molecules.  Diffusion constant is 
but one of many properties you need to look at if you want a valid model of 
propanol (or any molecule) - neat liquid structure, density, diffusion, DHvap, 
dipole moment, etc.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] miscelle formation using ligands only

2015-09-11 Thread Chetan Puri

I am using gromacs for the first time . I have installed gromacs 5.0.4
version and i want to check a miscelle is formed or not using 5 different
 ligands in different ratios. I have gone through all basic tutorials on
how to use gromacs ( lysosyme,protein-ligand).

But i am stuck with the problem of having ligands only for simulation due
to no force field and topology file.
  I have tried to use packmol to pack a cubic box with
all my different ligands in different ratios and generated a pdb file but
without making a topology file i am stuck.
  So if some one can suggest some possible ways  of doing it and i
don't have much computational background of manipulating various file
extensions of gromacs.
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[gmx-users] Cyclic peptide by using specbond.dat

2015-09-11 Thread Nikhil Maroli

*Dear Gromacs users*
*i have been having a bit of issues generating accurate topology for cyclic
peptide*

*i added extra terms in specbond.dat (Last Line)*
*as *

9

CYS SG 1 CYS SG 1 0.2 CYS2 CYS2

CYS SG 1 HEM FE 2 0.25 CYS2 HEME

CYS SG 1 HEM CAB 1 0.18 CYS2 HEME

CYS SG 1 HEM CAC 1 0.18 CYS2 HEME

HIS NE2 1 HEM FE 1 0.2 HIS1 HEME

MET SD 1 HEM FE 1 0.24 MET HEME

CO  C   1   HEMEFE  1   0.19CO  HEME
CYM SG  1   CYM SG  1   0.2 CYS2CYS2

*LYS C 1 ALA N 1 0.135 LYS ALA*


and my pdb file is as
SEQRES   1 A4  ALA LEU GLN LYS
LINK N   ALA A   1 C   LYS A   4
 1.34
ATOM  1  N   ALA A   1  -7.317  -0.819   1.765  1.00  0.00
  N
ATOM  2  H   ALA A   1  -6.725  -1.565   2.103  1.00  0.00
  H
ATOM  3  CA  ALA A   1  -6.768   0.542   1.865  1.00  0.00
  C
ATOM  4  HA  ALA A   1  -7.224   1.212   1.142  1.00  0.00
  H
ATOM  5  C   ALA A   1  -5.244   0.544   1.585  1.00  0.00
  C
ATOM  6  O   ALA A   1  -4.449   0.351   2.495  1.00  0.00
  O
ATOM  7  CB  ALA A   1  -7.092   1.097   3.262  1.00  0.00
  C
ATOM  8 HB1  ALA A   1  -6.673   0.442   4.029  1.00  0.00
  H
ATOM  9 HB1  ALA A   1  -8.168   1.171   3.407  1.00  0.00
  H
ATOM 10 HB1  ALA A   1  -6.651   2.089   3.375  1.00  0.00
  H
ATOM 11  N   LEU B   2  -4.781   0.766   0.348  1.00  0.00
  N
ATOM 12  H   LEU B   2  -3.776   0.718   0.265  1.00  0.00
  H
ATOM 13  CA  LEU B   2  -5.549   0.859  -0.902  1.00  0.00
  C
ATOM 14  HA  LEU B   2  -6.305   1.635  -0.790  1.00  0.00
  H
ATOM 15  C   LEU B   2  -6.247  -0.477  -1.208  1.00  0.00
  C
ATOM 16  O   LEU B   2  -5.673  -1.538  -0.993  1.00  0.00
  O
ATOM 17  CB  LEU B   2  -4.589   1.279  -2.034  1.00  0.00
  C
ATOM 18 HB1  LEU B   2  -4.111   2.220  -1.754  1.00  0.00
  H
ATOM 19 HB1  LEU B   2  -3.807   0.520  -2.117  1.00  0.00
  H
ATOM 20  CG  LEU B   2  -5.238   1.454  -3.426  1.00  0.00
  C
ATOM 21  HG  LEU B   2  -5.676   0.505  -3.738  1.00  0.00
  H
ATOM 22  CD1 LEU B   2  -6.340   2.525  -3.427  1.00  0.00
  C
ATOM 23 HD11 LEU B   2  -6.723   2.656  -4.440  1.00  0.00
  H
ATOM 24 HD12 LEU B   2  -5.940   3.476  -3.074  1.00  0.00
  H
ATOM 25 HD13 LEU B   2  -7.169   2.224  -2.789  1.00  0.00
  H
ATOM 26  CD2 LEU B   2  -4.160   1.833  -4.450  1.00  0.00
  C
ATOM 27 HD21 LEU B   2  -4.605   1.920  -5.442  1.00  0.00
  H
ATOM 28 HD22 LEU B   2  -3.391   1.060  -4.482  1.00  0.00
  H
ATOM 29 HD23 LEU B   2  -3.700   2.785  -4.180  1.00  0.00
  H
ATOM 30  N   GLN C   3  -7.497  -0.424  -1.671  1.00  0.00
  N
ATOM 31  H   GLN C   3  -7.910   0.469  -1.882  1.00  0.00
  H
ATOM 32  CA  GLN C   3  -8.323  -1.613  -1.897  1.00  0.00
  C
ATOM 33  HA  GLN C   3  -8.020  -2.397  -1.198  1.00  0.00
  H
ATOM 34  C   GLN C   3  -9.820  -1.324  -1.624  1.00  0.00
  C
ATOM 35  O   GLN C   3 -10.666  -1.591  -2.471  1.00  0.00
  O
ATOM 36  CB  GLN C   3  -8.045  -2.130  -3.325  1.00  0.00
  C
ATOM 37 HB1  GLN C   3  -8.470  -1.427  -4.044  1.00  0.00
  H
ATOM 38 HB2  GLN C   3  -6.967  -2.154  -3.497  1.00  0.00
  H
ATOM 39  CG  GLN C   3  -8.587  -3.552  -3.580  1.00  0.00
  C
ATOM 40 HG1  GLN C   3  -7.751  -4.250  -3.637  1.00  0.00
  H
ATOM 41 HG1  GLN C   3  -9.225  -3.868  -2.754  1.00  0.00
  H
ATOM 42  CD  GLN C   3  -9.400  -3.641  -4.869  1.00  0.00
  C
ATOM 43  OE1 GLN C   3  -8.993  -4.228  -5.857  1.00  0.00
  O
ATOM 44  NE2 GLN C   3 -10.567  -3.038  -4.913  1.00  0.00
  N
ATOM 45 HE21 GLN C   3 -11.082  -3.101  -5.769  1.00  0.00
  H
ATOM 46 HE22 GLN C   3 -10.883  -2.515  -4.103  1.00  0.00
  H
ATOM 47  N   LYS D   4 -10.243  -0.726  -0.500  1.00  0.00
  N
ATOM 48  H   LYS D   4 -11.247  -0.617  -0.471  1.00  0.00
  H
ATOM 49  CA  LYS D   4  -9.503  -0.233   0.679  1.00  0.00
  C
ATOM 50  HA  LYS D   4  -8.973   0.661   0.371  1.00  0.00
  H
ATOM 51  C   LYS D   4  -8.483  -1.241   1.259  1.00  0.00
  C
ATOM 52  O   LYS D   4  -8.735  -2.437   1.259  1.00  0.00
  O
ATOM 53  CB  LYS D   4 -10.517   0.166   1.774  1.00  0.00
  C
ATOM 54 HB1  LYS D   4 -11.377  -0.504   1.744  1.00  0.00
  H
ATOM 55 HB2  LYS D   4 -10.054   0.023   2.751  1.00  0.00
  H
ATOM 56  CG  LYS D   4 -10.987   1.632   1.713  1.00  0.00
  C
ATOM 57 HG1  LYS D   4 -11.669   1.806   2.546  1.00  0.00
  H
ATOM 58 HG2  LYS D   4 -10.120   2.277   1.858  1.00  0.00
  H
ATOM 59  CD  LYS D   4 -11.688   2.059   0.416  1.00  0.00
  C
ATOM 60 HD1  LYS D   4 -11.973   3.108   0.503  1.00  0.00
  H
ATOM 61 HD2  LYS D   4 -10.998   1.963  -0.422  1.00  0.00
  H

[gmx-users] How to create a spherocylindrical wall

[gmx-users] g_hbond

Re: [gmx-users] gromacs-5.1 with charmm36.ff

Re: [gmx-users] Cyclic peptide by using specbond.dat

Re: [gmx-users] Cyclic peptide by using specbond.dat

[gmx-users] Protein-ligand interaction calculation

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 137, Issue 61

Re: [gmx-users] Protein-ligand interaction calculation

Re: [gmx-users] g_hbond

Re: [gmx-users] How to create a spherocylindrical wall

Re: [gmx-users] Creating a box of water with density 1000 g/l

[gmx-users] miscelle formation using ligands only

[gmx-users] Cyclic peptide by using specbond.dat

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