date:20171227

Re: [gmx-users] More dihedrals generated than provided in the, force field & "No default Proper Dih. types" as a result

2017-12-27 Thread Timofey Tyugashev

28.12.2017 02:39, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 3
Date: Wed, 27 Dec 2017 13:46:37 -0500
From: Justin Lemkul
To:gmx-us...@gromacs.org
Subject: Re: [gmx-users] More dihedrals generated than provided in the
force field & "No default Proper Dih. types" as a result
Message-ID:
Content-Type: text/plain; charset=utf-8; format=flowed

On 12/27/17 9:39 AM, Timofey Tyugashev wrote:

I'm building a protein with a cubic [Fe4S4] cluster using parameters
from a published paper.
This parameters provide only two dihedral angles types (S-FE-SG-CB and
FE-S-FE-SG, where S and FE belong to the cluster and SG and CB belong
to the Cys residue).
GROMACS automatically generates far more dihedrals with types like
S-FE-S-FE (looks like all of them are inta-cluster) which are omitted
in the source paper and are explicitly stated to be redundant for MD.
However? grommp generates errors and stops:

ERROR 49 [file topol.top, line 32916]:
? No default Proper Dih. types

How to solve this problem?

pdb2gmx automatically generates all possible dihedrals. If they are not
necessary in your force field description, either remove the offending
lines from your topology or assign them dihedral parameters with force
constants equal to zero so they impose no force.

-Justin
Yes, right after sending the message I realised that the redundant 
dihedrals could be simply removed from the .top file. Seems to be 
running fine now.

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Re: [gmx-users] PROTEIN FOLDING

2017-12-27 Thread RAHUL SURESH

Hi,

migh be visualization error

Apply pbc

On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta 
wrote:

> Hi,
>
> I tried running the simulations for 50 ns.
>
> The protein breaks (but ligand remains in the active site of the protein
> and it is stable throughout )
>
> How to fix it?
>
> Thanks,
> Neha
>
> On Wed, Dec 20, 2017 at 6:28 PM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > Depends. If you're interested in local folding and there are SS motifs in
> > the region you're interested, then yes. If not, no. In terms of overall
> > folding of the entire protein, yes it surely can be an important
> analysis.
> >
> > J
> >
> > On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta 
> > wrote:
> >
> > > Thank you Joao and Aman.
> > >
> > > I have noted the points you have suggested.
> > >
> > > Do you think analyzing DSSP would help?
> > >
> > > Thanks,
> > > Neha
> > >
> > > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques <
> > > joao.m.a.henriq...@gmail.com> wrote:
> > >
> > > > "You can use various supporting tools from R language to debug your
> > > > trajectory but most third party software support NAMD and charmm
> > format.
> > > > You can use VMD to convert the trajectory to dcd and use R language
> > based
> > > > packages to read your trajectory"
> > > >
> > > > What? How is this useful or helpful? At most it confuses the OP even
> > > more.
> > > >
> > > > Also, the clustering analysis is unlikely to be what you want or need
> > at
> > > > this stage. Why overcomplicate? One of the simplest ways to check
> that
> > > > there are conformational changes on a given set of atoms is by doing
> a
> > > RMSD
> > > > analysis using the folded structure as the reference. The RMSD is
> > > somewhat
> > > > degenerate, but should suffice for this purpose. You can use an index
> > > file
> > > > to restrict the RMSD analysis to a particular subset of your system
> > (the
> > > > docking site, for example).
> > > >
> > > > You could look at the radius of gyration as well, Rg, as Aman Deep
> also
> > > > suggests. This can either be calculated on a subset of atoms or on
> the
> > > > entire protein. The latter could potentially be used to compare with
> > the
> > > > experimental reference obtained by SAXS, for example. Or you could
> > > > calculate the SAXS curve and get a better understanding of size and
> > shape
> > > > differences between your protein and the reference, but that's more
> > > > advanced stuff.
> > > >
> > > > J
> > > >
> > > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH <
> drrahulsur...@gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Also you must know, a lot analysis are available over the entire
> > manual
> > > > of
> > > > > Gromacs where all cannot be performed. Gromacs always provide you
> all
> > > > > necessary analysis but to choose which one is always your choice
> that
> > > > suits
> > > > > your simulation purpose.
> > > > >
> > > > >
> > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta <
> nehaphysic...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > >
> > > > > > Thank you for your prompt reply.
> > > > > >
> > > > > > By clustering analysis, are you talking about gmx cluster
> command?
> > > > > >
> > > > > > "over particular PC sub space"
> > > > > >
> > > > > > Could you please elaborate a bit?
> > > > > >
> > > > > > Thanks a lot once again.
> > > > > >
> > > > > > Thanks,
> > > > > > Neha
> > > > > >
> > > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH <
> > > drrahulsur...@gmail.com
> > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <
> > > nehaphysic...@gmail.com
> > > > >
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi gromacs users,
> > > > > > > >
> > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we
> > > view
> > > > > > > protein
> > > > > > > > folding?
> > > > > > > >
> > > > > > > > How to do it?
> > > > > > > >
> > > > > > > > I want to ascertain if there is any conformation change in
> > > protein
> > > > > > where
> > > > > > > > the ligand binds. Is it possible?
> > > > > > > >
> > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I
> > > want
> > > > to
> > > > > > > make
> > > > > > > > observation through MD simulation which is not obtained
> through
> > > > > > docking.
> > > > > > >
> > > > > > >
> > > > > > > You can perform Clustering analysis over particular PC sub
> space
> > to
> > > > > > measure
> > > > > > > the structural changes.
> > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > Can someone help me regarding this?
> > > > > > > >
> > > > > > > > Thank you very much in advance.
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > > Neha
> > > > > > > > --
> > > > > > > > Gromacs Users mailing list
> > > > > > > >
> > > > > > > > * Please search the archive at
> > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > >

Re: [gmx-users] PROTEIN FOLDING

2017-12-27 Thread Neha Gupta

Hi,

I tried running the simulations for 50 ns.

The protein breaks (but ligand remains in the active site of the protein
and it is stable throughout )

How to fix it?

Thanks,
Neha

On Wed, Dec 20, 2017 at 6:28 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Depends. If you're interested in local folding and there are SS motifs in
> the region you're interested, then yes. If not, no. In terms of overall
> folding of the entire protein, yes it surely can be an important analysis.
>
> J
>
> On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta 
> wrote:
>
> > Thank you Joao and Aman.
> >
> > I have noted the points you have suggested.
> >
> > Do you think analyzing DSSP would help?
> >
> > Thanks,
> > Neha
> >
> > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > "You can use various supporting tools from R language to debug your
> > > trajectory but most third party software support NAMD and charmm
> format.
> > > You can use VMD to convert the trajectory to dcd and use R language
> based
> > > packages to read your trajectory"
> > >
> > > What? How is this useful or helpful? At most it confuses the OP even
> > more.
> > >
> > > Also, the clustering analysis is unlikely to be what you want or need
> at
> > > this stage. Why overcomplicate? One of the simplest ways to check that
> > > there are conformational changes on a given set of atoms is by doing a
> > RMSD
> > > analysis using the folded structure as the reference. The RMSD is
> > somewhat
> > > degenerate, but should suffice for this purpose. You can use an index
> > file
> > > to restrict the RMSD analysis to a particular subset of your system
> (the
> > > docking site, for example).
> > >
> > > You could look at the radius of gyration as well, Rg, as Aman Deep also
> > > suggests. This can either be calculated on a subset of atoms or on the
> > > entire protein. The latter could potentially be used to compare with
> the
> > > experimental reference obtained by SAXS, for example. Or you could
> > > calculate the SAXS curve and get a better understanding of size and
> shape
> > > differences between your protein and the reference, but that's more
> > > advanced stuff.
> > >
> > > J
> > >
> > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH  >
> > > wrote:
> > >
> > > > Also you must know, a lot analysis are available over the entire
> manual
> > > of
> > > > Gromacs where all cannot be performed. Gromacs always provide you all
> > > > necessary analysis but to choose which one is always your choice that
> > > suits
> > > > your simulation purpose.
> > > >
> > > >
> > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta 
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > >
> > > > > Thank you for your prompt reply.
> > > > >
> > > > > By clustering analysis, are you talking about gmx cluster command?
> > > > >
> > > > > "over particular PC sub space"
> > > > >
> > > > > Could you please elaborate a bit?
> > > > >
> > > > > Thanks a lot once again.
> > > > >
> > > > > Thanks,
> > > > > Neha
> > > > >
> > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH <
> > drrahulsur...@gmail.com
> > > >
> > > > > wrote:
> > > > >
> > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <
> > nehaphysic...@gmail.com
> > > >
> > > > > > wrote:
> > > > > >
> > > > > > > Hi gromacs users,
> > > > > > >
> > > > > > > After MD simulation of protein-ligand complex for 5ns, can we
> > view
> > > > > > protein
> > > > > > > folding?
> > > > > > >
> > > > > > > How to do it?
> > > > > > >
> > > > > > > I want to ascertain if there is any conformation change in
> > protein
> > > > > where
> > > > > > > the ligand binds. Is it possible?
> > > > > > >
> > > > > > > We observe hydrogen bonds through molecular docking. Hence, I
> > want
> > > to
> > > > > > make
> > > > > > > observation through MD simulation which is not obtained through
> > > > > docking.
> > > > > >
> > > > > >
> > > > > > You can perform Clustering analysis over particular PC sub space
> to
> > > > > measure
> > > > > > the structural changes.
> > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Can someone help me regarding this?
> > > > > > >
> > > > > > > Thank you very much in advance.
> > > > > > >
> > > > > > > Thanks,
> > > > > > > Neha
> > > > > > > --
> > > > > > > Gromacs Users mailing list
> > > > > > >
> > > > > > > * Please search the archive at
> > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > before
> > > > > > > posting!
> > > > > > >
> > > > > > > * Can't post? Read http://www.gromacs.org/
> Support/Mailing_Lists
> > > > > > >
> > > > > > > * For (un)subscribe requests visit
> > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> > gmx-users
> > > > or
> > > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > > >
> > > > > > --
> > > > > > *Regards,*
> > > > > > *Rahul Suresh*
> > > > > > *Research Scholar*

Re: [gmx-users] Strange energy values with GMX 5.1, PME and Verlet

2017-12-27 Thread Mark Abraham

Hi,

On Thu, Dec 28, 2017 at 6:40 AM Diana Lousa  wrote:

> Dear all,
>
> For testing purposes, I performed a short simulation (10 ps) of a CL- and a
> Na+ ion in vacuum with gmx 5.1.4 and compared the Group and Verlet cutoff
> schemes. I ran gmx energy to monitor the interaction energy between the
> ions and obtained the following results:
>
> 1) Verlet
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Pressure   0.128465  0.04415.8209   -0.27251  (bar)
> Coul-SR:NA-NA  -244.832  0   -nan -4.68375e-14
> (kJ/mol)
> LJ-SR:NA-NA   0  0  0  0
> (kJ/mol)
> Coul-SR:NA-CL  -153.1937.432.7214   -43.0706
> (kJ/mol)
> LJ-SR:NA-CL 42.52521.720.95319.65428
> (kJ/mol)
> Coul-SR:CL-CL  -244.832  0   -nan -4.68375e-14
> (kJ/mol)
> LJ-SR:CL-CL   0  0  0  0
> (kJ/mol)
>
> 2) Group
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Pressure  0.0159313  0.03917.1949   0.303503  (bar)
> Coul-SR:NA-NA 0  0  0  0
> (kJ/mol)
> LJ-SR:NA-NA   0  0  0  0
> (kJ/mol)
> Coul-SR:NA-CL  -152.361  833.2265   -46.2306
> (kJ/mol)
> LJ-SR:NA-CL 42.1.922.587711.0263
> (kJ/mol)
> Coul-SR:CL-CL 0  0  0  0
> (kJ/mol)
> LJ-SR:CL-CL   0  0  0  0
> (kJ/mol)
>
> As you can see, the Coul-SR:NA-NA and Coul-SR:CL-CL have the value of
> -244.832 when using Verlet, which is very strange.


PME for Verlet and group is implemented differently. The various kinds of
atom pairs whose non-bonded interactions must be excluded can be computed
in different ways. The approach in the Verlet scheme is more efficient, but
does not reproduce that of the group scheme, But anyway since such
decomposition is physically meaningless, it doesn't matter.


> This does not happen
> when using Group cutoff or when using Verlet in GMX 4.5 (the value is 0 in
> these cases).
>

4.5 did not have such a scheme.


> GMX 2016 gives similar results to GMX 5.1.4:
>
> 3) Verlet GMX 2016:
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Pressure -0.0106255   0.2219.2119   0.756146  (bar)
> Coul-SR:NA-NA  -244.832  0   -nan -4.68375e-14
> (kJ/mol)
> LJ-SR:NA-NA   0  0  0  0
> (kJ/mol)
> Coul-SR:NA-CL  -150.9217.9 35.159   -45.7216
> (kJ/mol)
> LJ-SR:NA-CL 42.0629  225.166811.2282
> (kJ/mol)
> Coul-SR:CL-CL  -244.832  0   -nan -4.68375e-14
> (kJ/mol)
> LJ-SR:CL-CL   0  0  0  0
> (kJ/mol)
>
> I am not using GPUs, since I know you cannot monitor energy groups when
> using GPUs.
> Does anyone have any idea why this happens and what consequences does it
> have?
>

None.

Mark


>
> Here's the mdp:
>
> 
> define  =
> integrator  =  md
> tinit   =  0.0
> dt  =  0.002
> nsteps  =  5000
> nstcomm =  1
> nstxtcout   =  500
> xtc-precision   =  1000
> nstxout =  0
> nstvout =  0
> nstfout =  0
> nstlog  =  10
> nstenergy   =  1
>
> nstlist =  20
> ns_type =  grid
>
> ;PME
> rlist   = 1.0
> coulombtype = PME
> rcoulomb= 1.0
> fourierspacing  = 0.16
> pme_order   = 4
> vdwtype = cut-off
> rvdw= 1.0
> cutoff-scheme = Verlet ; or Group
>
> ; Energy monitoring
> energygrps  =  NA CL
>
> Tcoupl  =  v-rescale
> tc-grps =  Ion
> tau_t   =  0.10
> ref_t   =  300.0
>
> ; Isotropic pressure coupling is now of
> ; Pcoupl  =  berendsen
> Pcoupl  =  No
>
>
> ; lincs_
> constraint_algorithm=lincs
> lincs_order =  8
> constraints = none
> lincs-warnangle =  90
>
>
> Thanks in advance
> Best regards
>
> --
> Diana Lousa
> Post-doc
> Protein Modeling Laboratory
> ITQB/UNL
> Oeiras, Portugal
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe

[gmx-users] Strange energy values with GMX 5.1, PME and Verlet

2017-12-27 Thread Diana Lousa

Dear all,

For testing purposes, I performed a short simulation (10 ps) of a CL- and a
Na+ ion in vacuum with gmx 5.1.4 and compared the Group and Verlet cutoff
schemes. I ran gmx energy to monitor the interaction energy between the
ions and obtained the following results:

1) Verlet
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   0.128465  0.04415.8209   -0.27251  (bar)
Coul-SR:NA-NA  -244.832  0   -nan -4.68375e-14
(kJ/mol)
LJ-SR:NA-NA   0  0  0  0
(kJ/mol)
Coul-SR:NA-CL  -153.1937.432.7214   -43.0706
(kJ/mol)
LJ-SR:NA-CL 42.52521.720.95319.65428
(kJ/mol)
Coul-SR:CL-CL  -244.832  0   -nan -4.68375e-14
(kJ/mol)
LJ-SR:CL-CL   0  0  0  0
(kJ/mol)

2) Group
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure  0.0159313  0.03917.1949   0.303503  (bar)
Coul-SR:NA-NA 0  0  0  0
(kJ/mol)
LJ-SR:NA-NA   0  0  0  0
(kJ/mol)
Coul-SR:NA-CL  -152.361  833.2265   -46.2306
(kJ/mol)
LJ-SR:NA-CL 42.1.922.587711.0263
(kJ/mol)
Coul-SR:CL-CL 0  0  0  0
(kJ/mol)
LJ-SR:CL-CL   0  0  0  0
(kJ/mol)

As you can see, the Coul-SR:NA-NA and Coul-SR:CL-CL have the value of
-244.832 when using Verlet, which is very strange. This does not happen
when using Group cutoff or when using Verlet in GMX 4.5 (the value is 0 in
these cases).
GMX 2016 gives similar results to GMX 5.1.4:

3) Verlet GMX 2016:
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure -0.0106255   0.2219.2119   0.756146  (bar)
Coul-SR:NA-NA  -244.832  0   -nan -4.68375e-14
(kJ/mol)
LJ-SR:NA-NA   0  0  0  0
(kJ/mol)
Coul-SR:NA-CL  -150.9217.9 35.159   -45.7216
(kJ/mol)
LJ-SR:NA-CL 42.0629  225.166811.2282
(kJ/mol)
Coul-SR:CL-CL  -244.832  0   -nan -4.68375e-14
(kJ/mol)
LJ-SR:CL-CL   0  0  0  0
(kJ/mol)

I am not using GPUs, since I know you cannot monitor energy groups when
using GPUs.
Does anyone have any idea why this happens and what consequences does it
have?


Here's the mdp:


define  =
integrator  =  md
tinit   =  0.0
dt  =  0.002
nsteps  =  5000
nstcomm =  1
nstxtcout   =  500
xtc-precision   =  1000
nstxout =  0
nstvout =  0
nstfout =  0
nstlog  =  10
nstenergy   =  1

nstlist =  20
ns_type =  grid

;PME
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0
fourierspacing  = 0.16
pme_order   = 4
vdwtype = cut-off
rvdw= 1.0
cutoff-scheme = Verlet ; or Group

; Energy monitoring
energygrps  =  NA CL

Tcoupl  =  v-rescale
tc-grps =  Ion
tau_t   =  0.10
ref_t   =  300.0

; Isotropic pressure coupling is now of
; Pcoupl  =  berendsen
Pcoupl  =  No


; lincs_
constraint_algorithm=lincs
lincs_order =  8
constraints = none
lincs-warnangle =  90


Thanks in advance
Best regards

-- 
Diana Lousa
Post-doc
Protein Modeling Laboratory
ITQB/UNL
Oeiras, Portugal
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Osmotic Pressure Calculations and fixed reference values of walls

2017-12-27 Thread Justin Lemkul




On 12/26/17 7:53 AM, Mandar Kulkarni wrote:

Dear All,
I am performing osmotic pressure simulations using 30 nucleoside molecules
using 1D flat bottom restraints along Z-axis(Zmin and Zmax). I am using
GROMACS 5.0.7 version and reference coordinates are provided using -r
option in grompp.
The osmotic pressure runs are performed under NPT conditions with
semi-isotropic pressure coupling. I am calculating osmotic pressure using
C-program which simply calculates forces on heavy atoms of nucleosides
attempting to cross the Zmin and Zmax limits.

I have searched archived posts, however, I am confused about possible
implementation and post-processing in the present case. Any help will be
really helpful to solve the following issues.

1. The upper and lower limits of the flat bottom restraints are defined
while starting the simulations using static reference frame. Although
|Zmax-Zmin|
will be constant, is it correct to assume fixed minimum(Zmin) and
maximum(Zmax) limits?


Such calculations are usually performed with a static z-dimension, e.g 
incompressible along that axis. In that case, Zmin and Zmax are (and 
should be) fixed.



2. During post-processing when one centers the trajectory and correct PBC
for nucleoside molecules (trjconv -pbc mol -ur compact -center options), is
it appropriate to assume the same Zmin and Zmax values at t=0 throughout
the analysis?


You shouldn't have to use any complex trjconv command. Just make 
molecules whole and that should be correct. No additional centering is 
required; your molecules stay in the central volume anyway, and you 
don't want to shift coordinates when relying on fixed points in space 
for computing your osmotic pressure forces.


-Justin


3. The GROMACS source code section below calculates flat-bottom restraint
forces

  for (m = 0; (m < DIM); m++)
 {
 f[ai][m]   += fm[m];
 /* Here we correct for the pbc_dx which included rdist */
 vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];

 }

How can we print force f[ai][m] at each time step to separate file? I
assume it might be not straightforward to print these forces, but a short
general guideline might help me to achieve the objective.

Sorry for so many questions and Thanks in advance.
Also, Wish you all happy new year in advance.

Best Regards,
Mandar Kulkarni,
Pusan National University, South Korea


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] regarding calculation of intra-residue energy

2017-12-27 Thread Justin Lemkul




On 12/26/17 1:34 PM, Saumyak Mukherjee wrote:

Dear all,

I have simulated myoglobin in water system. Now, I want to calculate the
self interaction energy (Coulomb) of the protein. In that case shall I
consider the interaction between the OE1 and OE2 atoms in glutamte, or
other such pairs?

Including all pairs, except the bonded pairs, the average self-energy of
the protein is coming as 8108 kT from my program. Is this value plausible?

Any comment/suggestion is appreciated.


First- and second-neighbor interactions are not included in standard 
force fields, so if your calculation includes them, you're going to get 
something that the force field is not designed to describe. Use the same 
exclusions as the force field expects.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] More dihedrals generated than provided in the force field & "No default Proper Dih. types" as a result

2017-12-27 Thread Justin Lemkul




On 12/27/17 9:39 AM, Timofey Tyugashev wrote:
I'm building a protein with a cubic [Fe4S4] cluster using parameters 
from a published paper.
This parameters provide only two dihedral angles types (S-FE-SG-CB and 
FE-S-FE-SG, where S and FE belong to the cluster and SG and CB belong 
to the Cys residue).
GROMACS automatically generates far more dihedrals with types like 
S-FE-S-FE (looks like all of them are inta-cluster) which are omitted 
in the source paper and are explicitly stated to be redundant for MD. 
However  grommp generates errors and stops:


ERROR 49 [file topol.top, line 32916]:
  No default Proper Dih. types

How to solve this problem?


pdb2gmx automatically generates all possible dihedrals. If they are not 
necessary in your force field description, either remove the offending 
lines from your topology or assign them dihedral parameters with force 
constants equal to zero so they impose no force.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] More dihedrals generated than provided in the force field & "No default Proper Dih. types" as a result

2017-12-27 Thread Timofey Tyugashev

I'm building a protein with a cubic [Fe4S4] cluster using parameters 
from a published paper.
This parameters provide only two dihedral angles types (S-FE-SG-CB and 
FE-S-FE-SG, where S and FE belong to the cluster and SG and CB belong to 
the Cys residue).
GROMACS automatically generates far more dihedrals with types like 
S-FE-S-FE (looks like all of them are inta-cluster) which are omitted in 
the source paper and are explicitly stated to be redundant for MD. 
However  grommp generates errors and stops:


ERROR 49 [file topol.top, line 32916]:
  No default Proper Dih. types

How to solve this problem?
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[gmx-users] dielectric constant effect on protein, dna, water interface

2017-12-27 Thread Sarath Chandra

Fellow users,

I am working on a Protein-DNA complex and I have a question regarding the
electrostatic interaction energies calculated at the interface of protein,
DNA and water. I am using amber99sb+parambsc0  forcefield for my system
with TIP3P water simulated using gromacs4.6.4.

I understand that the additive forcefield does not capture polarizibility
well. I have already referred to articles on PME but it is not clear if the
PME takes into account the dielectric constant change at the protein, DNA,
water interface. During the electrostatic forces calculation is this
captured by calculation of local dipole moments on fly? This is critical to
understand the effect of protein on DNA structural properties.

I look forward to your reply.

Best regards,

Sarath
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Re: [gmx-users] More dihedrals generated than provided in the, force field & "No default Proper Dih. types" as a result

Re: [gmx-users] PROTEIN FOLDING

Re: [gmx-users] PROTEIN FOLDING

Re: [gmx-users] Strange energy values with GMX 5.1, PME and Verlet

[gmx-users] Strange energy values with GMX 5.1, PME and Verlet

Re: [gmx-users] Osmotic Pressure Calculations and fixed reference values of walls

Re: [gmx-users] regarding calculation of intra-residue energy

Re: [gmx-users] More dihedrals generated than provided in the force field & "No default Proper Dih. types" as a result

[gmx-users] More dihedrals generated than provided in the force field & "No default Proper Dih. types" as a result

[gmx-users] dielectric constant effect on protein, dna, water interface

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