[gmx-users] Representative structure from MD trajectories

2011-09-09 Thread bipin singh
Hello,

I have constructed a 2-d FEL using PC1 and PC2 as the reaction
coordinates(by using g_sham).
>From this 2-d FEL, I extracted the PC1 and PC2 (principal components)
values corresponding to minimum free energy.
Then I extracted the time during which system possess these PC's
values( by looking at PC Vs time plot).
Now I want to extract representative structures from these time
length(for eg. 40ns to 70 ns) of MD trajectories.


This question had been discussed previously but I am not able to find
a consensus solution:

There are three approaches discussed in the previous posts:
(1)Use g_cluster with options -av(writes average) -cl and then
minimize the structure
(2)Use g_covar -av, and then minimize the average structure.
(3)Use g_rmsf -ox, and minimize the structure


Please suggest which approach should be used for this purpose.




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Re: [gmx-users] radial distribution function

2011-09-09 Thread Justin A. Lemkul



lina wrote:



On Sat, Sep 10, 2011 at 3:35 AM, Moeed > wrote:


Dear users,

I have created radial distribution function plot for Carbon atoms in
a system containing polymer chains. I see some little jumps between
first and second peak.
I need your help to comment on how this behavior can be justified
(or if the plot is wrong).

g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx 


Thank you in advance.


I think your figure is fine.



I think, based on information given in subsequent messages, that there is 
insufficient data collection to assess whether this RDF plot is as meaningful as 
it could be.  There is nothing glaringly wrong, but the roughness is due to 
insufficient sampling.




You just need how to proper interpret your figures, truly understand 
what the "radial distribution" means.
 


I think it inappropriate to suggest that the OP does not understand the concept 
behind the figure; some guidance, perhaps is necessary, but nothing more.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] radial distribution function

2011-09-09 Thread lina
On Sat, Sep 10, 2011 at 3:35 AM, Moeed  wrote:

> Dear users,
>
> I have created radial distribution function plot for Carbon atoms in a
> system containing polymer chains. I see some little jumps between first and
> second peak.
> I need your help to comment on how this behavior can be justified (or if
> the plot is wrong).
>
> g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
> Thank you in advance.
>

I think your figure is fine.

You just need how to proper interpret your figures, truly understand what
the "radial distribution" means.


>
>
>
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lina
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Re: [gmx-users] radial distribution function

2011-09-09 Thread Justin A. Lemkul



Moeed wrote:



On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul > wrote:




Moeed wrote:

Thank you Justin for your reply. Simulation is 5 ns long (
before this a 500 ps NVT was done as equilibration) and total
energy has been equilibrated after around 3 ns.

 -b is set to 4000 that is the last 1 ns has been used for rdf.


For all but the simplest systems this simulation length and data
analysis period is insufficient.  How big is your polymer?  Proper
sampling may take tens to hundreds of ns of data collection.

Thanks. There are about 250 backbone carbons on 4 chains. Molecular 
weight of each chains is around 3700 g/mol. I have been looking at total 
energies and densities to equilibrate by checking sign change of 
Tot-Drift for these properties before 5 ns. I actually dont see a big 
change in energies. Is there any criteria to check on this using RMSD or 
error? (so far I have been using sing change of Tot-Drift).


Please guide me. Thank you.
 


The criteria should be whatever experimental observables you wish to reproduce. 
 Once those have converged to reliable values, you've done enough simulation. 
Total energy should always remain (relatively) constant throughout a simulation; 
it is a relatively insensitive measure for assessing equilibrium.


Even simple, robust protein systems are not reliably converged in 5 ns.  I 
sincerely doubt that large polymer chains are either, especially with the 
possibility of entanglement or configurational changes.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] radial distribution function

2011-09-09 Thread Moeed
On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul  wrote:

>
>
> Moeed wrote:
>
>> Thank you Justin for your reply. Simulation is 5 ns long ( before this a
>> 500 ps NVT was done as equilibration) and total energy has been equilibrated
>> after around 3 ns.
>>
>>  -b is set to 4000 that is the last 1 ns has been used for rdf.
>>
>>
> For all but the simplest systems this simulation length and data analysis
> period is insufficient.  How big is your polymer?  Proper sampling may take
> tens to hundreds of ns of data collection.
>
> Thanks. There are about 250 backbone carbons on 4 chains. Molecular weight
of each chains is around 3700 g/mol. I have been looking at total energies
and densities to equilibrate by checking sign change of Tot-Drift for these
properties before 5 ns. I actually dont see a big change in energies. Is
there any criteria to check on this using RMSD or error? (so far I have been
using sing change of Tot-Drift).

Please guide me. Thank you.


> -Justin
>
>  Best,
>> moeed
>>
>>
>> On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Moeed wrote:
>>
>>Dear users,
>>
>>I have created radial distribution function plot for Carbon
>>atoms in a system containing polymer chains. I see some little
>>jumps between first and second peak.
>>I need your help to comment on how this behavior can be
>>justified (or if the plot is wrong).
>>
>>g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
>>
>>
>>How long is the sampling?  In the absence of -e and with -b being
>>hidden from us for some unknown reason, it's hard to guess.  I'd say
>>your simulation just isn't fully converged, although for complex
>>systems that can be a challenge anyway. Nothing unusual.
>>
>>-Justin
>>
>>-- ==**__==
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin
>>
>> 
>> >
>>
>>==**__==
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>> 
>> >
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>>
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search
>>
>> >
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>>> >.
>>
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>> 
>> >
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] dialanine using charmm27 ff

2011-09-09 Thread Sandeep Somani
Hi Mark

It worked ! pdb2gmx is now properly processing the pdb, and moreover the
potential energy from gmx is within 1.27 kJ/mol of that from Charmm. More on
energy comparison shortly.

However, further tinkering of the rtp and pdb file was required to generate
the topology:
1.
The original rtp entry which had HT1/2/3 for the methyl hydrogens was giving
the error
"
Fatal error:
Atom H1 in residue ACE 1 was not found in rtp entry ACE with 6 atoms
while sorting atoms.
 "
even though neither rtp nor pdb had H1 atom. I do not understand why it was
insisting on H1/2/3. It worked upon changing HT1/2/3 to H1/2/3.

2.
I changed bond entry  'N CAT'  -> 'N CT' in rtp entry of CT3. Guess CAT was
a typo.

3.
The improper dihedral in CT3
'  -C  CT N   -O ; commented to match with charmm psf '
was absent from the charmm psf. So I commented it.

fyi - final pdb and rtp entries are listed below.

Now, regarding the energies, I compared the different bonded and non-bonded
energy components from charmm with those from gmx.
Bonds, dihedral and coulomb energies matched to within 0.01 kJ/mol which was
great!
The discrepancy is in angles (U-B) where gmx value is higher by 1.6652
kJ/mol and LJ where gmx is lower by 0.459 kJ/mol.

Any idea on how to fix the angles (not too bothered by LJ) ?
I checked that the total number of angles in charmm psf and gmx top are the
same (=54), but havn't yet compared individual entries.

btw, would you (or someone else here) have a sample charmm (inp, crd, psf)
and gmx (mdp, gro, top) files where the two energies show a better match? It
would help me with this troubleshooting.

Thanks for your help
Sandeep

final rtp entries
[ ACE ]
 [ atoms ]
   CT3 CT3 -0.270  0
   H1 HA  0.090   1
   H2 HA  0.090   2
   H3 HA  0.090   3
   C   C   0.510   4
   O   O   -0.510  5
 [ bonds ]
   C   CT3
   C   +N
   CT3 H1
   CT3 H2
   CT3 H3
   O   C
 [ impropers ]
   C   CT3 +N  O

[ CT3 ]
; this can also be done with the .c.tdb, but the atom naming is different
; and this can matter
 [ atoms ]
   N   NH1 -0.470  0
   HN  H   0.310   1
   CT  CT3 -0.110  2
   H1 HA  0.090   3
   H2 HA  0.090   4
   H3 HA  0.090   5
 [ bonds ]
   -C  N
   N   HN
   N   CT
   CT  H1
   CT  H2
   CT  H3
 [ impropers ]
   N   -C  CT HN
;  -C  CT N   -O ; commented to match with charmm psf
==final rtp entries==

==final pdb==
REMARK  NONE *

REMARK   DATE: 8/10/11  5:30:23  CREATED BY USER: ss2029

ATOM  1  CT3 ACE 1  -2.160   0.537   0.930  1.00  0.00  DIAL
ATOM  2  H1  ACE 1  -2.466   0.003   0.005  1.00  0.00  DIAL
ATOM  3  H2  ACE 1  -2.562   1.572   0.910  1.00  0.00  DIAL
ATOM  4  H3  ACE 1  -2.562   0.001   1.816  1.00  0.00  DIAL
ATOM  5  C   ACE 1  -0.672   0.582   1.009  1.00  0.00  DIAL
ATOM  6  O   ACE 1  -0.105   1.128   1.954  1.00  0.00  DIAL
ATOM  7  N   ALA 2   0.000   0.000   0.000  1.00  0.00  DIAL
ATOM  8  HN  ALA 2  -0.453  -0.444  -0.769  1.00  0.00  DIAL
ATOM  9  CA  ALA 2   1.459   0.000   0.000  1.00  0.00  DIAL
ATOM 10  HA  ALA 2   1.812  -0.497   0.897  1.00  0.00  DIAL
ATOM 11  CB  ALA 2   1.949  -0.834  -1.207  1.00  0.00  DIAL
ATOM 12  HB1 ALA 2   1.514  -1.854  -1.155  1.00  0.00  DIAL
ATOM 13  HB2 ALA 2   1.628  -0.373  -2.167  1.00  0.00  DIAL
ATOM 14  HB3 ALA 2   3.056  -0.932  -1.214  1.00  0.00  DIAL
ATOM 15  C   ALA 2   2.096   1.401   0.000  1.00  0.00  DIAL
ATOM 16  O   ALA 2   1.425   2.432   0.000  1.00  0.00  DIAL
ATOM 17  N   ALA 3   3.451   1.458   0.000  1.00  0.00  DIAL
ATOM 18  HN  ALA 3   3.954   0.594   0.000  1.00  0.00  DIAL
ATOM 19  CA  ALA 3   4.276   2.664   0.000  1.00  0.00  DIAL
ATOM 20  HA  ALA 3   4.065   3.236  -0.897  1.00  0.00  DIAL
ATOM 21  CB  ALA 3   3.864   3.539   1.207  1.00  0.00  DIAL
ATOM 22  HB1 ALA 3   2.776   3.756   1.155  1.00  0.00  DIAL
ATOM 23  HB2 ALA 3   4.063   3.014   2.167  1.00  0.00  DIAL
ATOM 24  HB3 ALA 3   4.407   4.508   1.214  1.00  0.00  DIAL
ATOM 25  C   ALA 3   5.791   2.399   0.000  1.00  0.00  DIAL
ATOM 26  O   ALA 3   6.597   3.328   0.000  1.00  0.00  DIAL
ATOM 27  N   CT3 4   6.175   1.110   0.000  1.00  0.00  DIAL
ATOM 28  HN  CT3 4   5.528   0.351   0.000  1.00  0.00  DIAL
ATOM

Re: [gmx-users] (no subject)

2011-09-09 Thread Justin A. Lemkul



Алексей Раевский wrote:
Hi. I've look through the manual and didn't find an answer on my 
question: i've got a trajectory and i want to convert it in *.pdb with 
such parameters of index file [all atoms within a sphere with a chosen 
radius around selected atom]. What can i do? Thank you




Use g_select to generate the index group and trjconv to write the file in the 
format (and with the contents) that you want.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] (no subject)

2011-09-09 Thread Алексей Раевский
Hi. I've look through the manual and didn't find an answer on my question:
i've got a trajectory and i want to convert it in *.pdb with such parameters
of index file [all atoms within a sphere with a chosen radius around
selected atom]. What can i do? Thank you


-- 
*С уважением!


***
*

Nemo me impune lacessit*
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Re: [gmx-users] gromacs 4.5 tools for trajectory analysis

2011-09-09 Thread Justin A. Lemkul



Hasan haska wrote:

Dear gromacs users,

I loaded my .psf and then loaded .pdb file into psf  in VMD then used 
the command “ topo writegmxtop myfile.top” in tk console. I finally 
generated a gromacs .top file successfully. I want to use gromacs 4.5 
tools for trajectory analysis with namd dcd and pdb files. But how can I 
generate a gromacs tpr file using this .top file ? Can you please give 
me the information about generating tpr file ? 
 


Please read the manual and the many tutorials on the Gromacs website.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] radial distribution function

2011-09-09 Thread Justin A. Lemkul



Moeed wrote:
Thank you Justin for your reply. Simulation is 5 ns long ( before this a 
500 ps NVT was done as equilibration) and total energy has been 
equilibrated after around 3 ns.


 -b is set to 4000 that is the last 1 ns has been used for rdf.



For all but the simplest systems this simulation length and data analysis period 
is insufficient.  How big is your polymer?  Proper sampling may take tens to 
hundreds of ns of data collection.


-Justin


Best,
moeed

On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul > wrote:




Moeed wrote:

Dear users,

I have created radial distribution function plot for Carbon
atoms in a system containing polymer chains. I see some little
jumps between first and second peak.
I need your help to comment on how this behavior can be
justified (or if the plot is wrong).

g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx


How long is the sampling?  In the absence of -e and with -b being
hidden from us for some unknown reason, it's hard to guess.  I'd say
your simulation just isn't fully converged, although for complex
systems that can be a challenge anyway. Nothing unusual.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] gromacs 4.5 tools for trajectory analysis

2011-09-09 Thread Hasan haska
Dear gromacs users,


I loaded my .psf and then loaded .pdb file into psf  in VMD then used the 
command “ topo writegmxtop myfile.top” in tk console. I finally generated a 
gromacs .top file successfully. I want to use gromacs 4.5 tools for trajectory 
analysis with namd dcd and pdb files. But how can I generate a gromacs tpr file 
using this .top file ? Can you please give me the information about generating 
tpr file ?  
 
Thanks a lot for your help.-- 
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[gmx-users] Help OPLS-AA system explodes

2011-09-09 Thread joselin peredo
Dear Gromacs Users:
I've been working with small unsaturated hydrocarbons using OPLS-AA with NVT
calculations using box dimensions according to : x=y & z=3x centered in
1/2x,1/2y,1/2z in order to obtain surface tension. My system expands at the
begging of the mdrun calculation until it occupies the whole box uniformly.
The mdp file i'm using its:

; VARIOUS PREPROCESSING OPTIONS
title= Yo
cpp  = /usr/bin/cpp
include  =
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.003
nsteps   = 40
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=

; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
;bd-temp  = 300
;bd-fric  = 0
;ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 100
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 1000
nstvout  = 1000
nstfout  = 1000
; Checkpointing helps you continue after crashes
nstcheckpoint= 1000
; Output frequency for energies to log file and energy file
nstlog   = 50
nstenergy= 50
; Output frequency and precision for xtc file
nstxtcout= 50
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps   =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 1.4
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.4
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r= 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch  = 0
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0
; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl   = berendsen
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 330
; Pressure coupling
Pcoupl   = no
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0
; Random seed for Andersen thermostat
ondersen_seed= 815131




; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing= no
; Number of time points to use for specifying annealing in each group
annealing_npoints=
; List 

Re: [gmx-users] radial distribution function

2011-09-09 Thread Moeed
Thank you Justin for your reply. Simulation is 5 ns long ( before this a 500
ps NVT was done as equilibration) and total energy has been equilibrated
after around 3 ns.

 -b is set to 4000 that is the last 1 ns has been used for rdf.

Best,
moeed

On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul  wrote:

>
>
> Moeed wrote:
>
>> Dear users,
>>
>> I have created radial distribution function plot for Carbon atoms in a
>> system containing polymer chains. I see some little jumps between first and
>> second peak.
>> I need your help to comment on how this behavior can be justified (or if
>> the plot is wrong).
>>
>> g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
>>
>
> How long is the sampling?  In the absence of -e and with -b being hidden
> from us for some unknown reason, it's hard to guess.  I'd say your
> simulation just isn't fully converged, although for complex systems that can
> be a challenge anyway. Nothing unusual.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] radial distribution function

2011-09-09 Thread Justin A. Lemkul



Moeed wrote:

Dear users,

I have created radial distribution function plot for Carbon atoms in a 
system containing polymer chains. I see some little jumps between first 
and second peak.
I need your help to comment on how this behavior can be justified (or if 
the plot is wrong).


g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx 



How long is the sampling?  In the absence of -e and with -b being hidden from us 
for some unknown reason, it's hard to guess.  I'd say your simulation just isn't 
fully converged, although for complex systems that can be a challenge anyway. 
Nothing unusual.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] radial distribution function

2011-09-09 Thread Moeed
Dear users,

I have created radial distribution function plot for Carbon atoms in a
system containing polymer chains. I see some little jumps between first and
second peak.
I need your help to comment on how this behavior can be justified (or if the
plot is wrong).

g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
Thank you in advance.
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Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

2011-09-09 Thread Justin A. Lemkul



Shilpi Chaurasia wrote:
 I am trying to pull apart two dimers of tubulin protein joined 
together, to form two separate dimers by steered molecular dynamics 
using Pull code. The objective is to separate the dimers by pulling 
along one axis only (Y axis). I ran the simulation for 25 ps and it 
accomplished well but while visualizing the trajectory in VMD, in the 
very beginning (first frame), dimers are at distance which is much 
greater than expected. I expected that in first frame they should not 
have separated too much (i.e. in just 1 ps, they are at greater 
distance) I guess this is unusual. Please let me know where I am doing 
wrong? I have used the following pull code:




Actual numbers would help.  Is your initial configuration simply split across 
periodic boundaries?  If the initial distance is roughly equivalent to one of 
the box vectors, then that's the case.  Otherwise, please provide real data and 
check to make sure your pull groups are what you think they are.



pull= umbrella
pull_geometry   = distance
pull_dim= N N Y


Note that you're not actually pulling along Y as you state above.  Here, you're 
pulling along Z.  Perhaps that's one issue.


-Justin

pull_start  = yes 
pull_init1  = 0.0

pull_ngroups= 1
pull_group0 = dimer_ref   ; reference group (based on 
index file)

pull_group1 = dimer_pull   ; pull group
pull_rate1  = 0.1  
pull_k1 = 1000 
pull_nstfout= 10  
pull_nstxout= 10


best regards,
Shilpi Chaurasia



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

2011-09-09 Thread Shilpi Chaurasia
 I am trying to pull apart two dimers of tubulin protein joined together, to 
form two separate dimers by steered molecular dynamics using Pull code. The 
objective is to separate the dimers by pulling along one axis only (Y axis). I 
ran the simulation for 25 ps and it accomplished well but while visualizing the 
trajectory in VMD, in the very beginning (first frame), dimers are at distance 
which is much greater than expected. I expected that in first frame they should 
not have separated too much (i.e. in just 1 ps, they are at greater distance) I 
guess this is unusual. Please let me know where I am doing wrong? I have used 
the following pull code:

pull    = umbrella
pull_geometry   = distance
pull_dim    = N N Y
pull_start  = yes  
pull_init1  = 0.0
pull_ngroups    = 1
pull_group0 = dimer_ref   ; reference group (based on index 
file)
pull_group1 = dimer_pull   ; pull group
pull_rate1  = 0.1   
pull_k1 = 1000  
pull_nstfout    = 10   
pull_nstxout    = 10

best regards,
Shilpi Chaurasia
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[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

2011-09-09 Thread Yun Shi
Hi Alan,

I am not sure if my acpype version is not updated. But I did try, and it
behaved the same as amb2gmx.pl for dihedrals.

Yun


Or why not trying acpype?

Cheers,

Alan

On 9 September 2011 07:37, Mark Abraham  wrote:

>  On 9/09/2011 4:21 PM, Yun Shi wrote:
>
> Hi all,
>
> I understand this problem has been discussed before, but it seems no
> conclusion has been drawn.
>
>
> Someone needs to do some work and report back :-)
>
>
>
> GLYCAM force field assigns negative force constants to some dihedrals, and
> when amb2gmx.pl was used to convert prmtop file to gromacs top file, these
> negative values seem to be ignored. Some people proposed that we change
the
> code in amb2gmx.pl, that is:
>
> ...
>
>   # get all force constants for each line of a dihedral #
>   my $lines = $i -1 +$numijkl;
>   for(my $j=$i;$j<=$lines;$j++){
> my $period = abs($pn{$j});
> if($pk{$j}>0) {
>   $V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
> }
>
> ...
>
> the "$pk{$j}>0" is modified to "$pk{$j}!=0".
>
> Others suggest to modify the original prmtop file, that is, to remove the
> negative signs, and correspondingly, change the phase shift from 0 to 180.
> Then amb2gmx.pl could be used to correctly convert the topology.
>
> I am wondering if the first approach has been validated, since the second
> one seems complicated and laborious to carry out.
>
>
> Seems like a straightforward job for regular expression replacement using
> sed/perl/python/whatever. It might even be a one-liner.
>
> Mark
>
> --
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--
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Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

2011-09-09 Thread Mark Abraham

On 9/09/2011 10:01 PM, Marcin Zielinski wrote:

Ok, giving -DGMX_ACCELERATE=Power6 results with:

src/config.h
/* Define to a macro mangling the given C identifier (in lower and upper
   case), which must not contain underscores, for linking with 
Fortran. */

#define F77_FUNC(name,NAME)  name ##

/* As F77_FUNC, but for C identifiers containing underscores. */
#define F77_FUNC_(name,NAME) name ##

which, after issuing make, results with an error message at the very 
beginning:
"/home/grmcs454/gromacsdir/test-build/src/config.h", line 45.39: 
1506-210 (S) The ## operator requires two operands.
"/home/grmcs454/gromacsdir/test-build/src/config.h", line 48.39: 
1506-210 (S) The ## operator requires two operands.


I checked cmake/CMakeLists.txt and '##' are put explicitly therefor 
they will be present with _
afterwards or without it, thus giving this error every time You put 
Power6 or Fortran option on.

As far as I understand.


They make sense if $suffix is non-empty, but it can be empty, so it 
looks like someone didn't code this right. If the patch below works, let 
me know and I'll fix the source version.


Mark

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f26734d..a59a1de 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -636,13 +636,24 @@ if(GMX_FORTRAN OR GMX_POWER6)
 if(prefix)
   set(prefix "${prefix} ##")
 endif(prefix)
+if(suffix)
+  set(suffix "## ${suffix}")
+  if(extrasuffix)
+   set(extrasuffix "${suffix}${extrasuffix}")
+  endif(extrasuffix)
+else(suffix)
+  if(extrasuffix)
+   # Don't know if this is needed, but it can't hurt
+   set(extrasuffix "## ${extrasuffix}")
+  endif(extrasuffix)
+endif(suffix)

 if(isupper)
-set(F77_FUNCDEF   "${prefix} NAME ## ${suffix}")
-set(F77_FUNCDEF_  "${prefix} NAME ## ${suffix}${extrasuffix}")
+set(F77_FUNCDEF   "${prefix} NAME ${suffix}")
+set(F77_FUNCDEF_  "${prefix} NAME ${extrasuffix}")
 else(isupper)
-set(F77_FUNCDEF   "${prefix} name ## ${suffix}")
-set(F77_FUNCDEF_  "${prefix} name ## ${suffix}${extrasuffix}")
+set(F77_FUNCDEF   "${prefix} name ${suffix}")
+set(F77_FUNCDEF_  "${prefix} name ${extrasuffix}")
 endif(isupper)
 else(GMX_FORTRAN OR GMX_POWER6)
 set(F77_FUNCDEF   "name ## _")

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Re: [gmx-users] md.mdp file GPU one

2011-09-09 Thread lina
On Fri, Sep 9, 2011 at 8:48 PM, Justin A. Lemkul  wrote:

>
>
> lina wrote:
>
>> Hi,
>>
>>
>> are there someone love to share one md.mdp file for GPU version?
>>
>>
> All the details are here:
>
> http://www.gromacs.org/**Downloads/Installation_**
> Instructions/GPUs?highlight=**gpu
>
> The benchmark archive has example .mdp files that you can tweak.
>

Thanks. ( From those warnings, started to realize its limitations, no plan
to try further recently. ^_^ )


>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
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lina
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Re: [gmx-users] Density

2011-09-09 Thread Justin A. Lemkul



vferra...@units.it wrote:

Dear all,

I want to calculate the density of my system and visualize it during the 
simulation time. I've tried with g_density and with g_energy but in all 
the cases the density calculated is the average density all along the 
simulation and not the density of all the system in each step of the 
trajectory. How can I compute what I need?




g_energy should have printed an energy.xvg file that contains values printed 
every nstenergy steps.  It will not necessarily agree exactly with the average 
printed by g_energy, since the .edr file is accurate over all MD steps but the 
.xvg file contains data saved at only the requested output frequency.  So unless 
you set nstenergy = 1, you will not get density values over every step.


-Justin


Thanks a lot.
Valerio


This message was sent using IMP, the Internet Messaging Program.




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Density

2011-09-09 Thread vferrario

Dear all,

I want to calculate the density of my system and visualize it during  
the simulation time. I've tried with g_density and with g_energy but  
in all the cases the density calculated is the average density all  
along the simulation and not the density of all the system in each  
step of the trajectory. How can I compute what I need?


Thanks a lot.
Valerio


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Re: [gmx-users] Re: g_sas of ligands

2011-09-09 Thread Justin A. Lemkul



Steven Neumann wrote:
Was my question not clear or noone can help me? I am wondering whether 
calculations of ligand hydrophobic SAS (decrease during the 
simualtion) can be result of binding to protein? 
 



Presumably it's due to both aggregation and binding to the protein, if, in fact 
both phenomena occur.  The extent of each effect will vary with time and you may 
have to analyze each ligand separately (i.e. do 30 calculations) to gather the 
detail you need.  In the absence of seeing the commands used to calculate the 
quantities you did, it's hard to comment further on any of the other points.


-Justin

 
On Fri, Sep 9, 2011 at 8:23 AM, Steven Neumann > wrote:


Dear Gromacs Users,
 
I am calculating SAS using g_sas of ligands in my system: protein,

30 ligands in water. The hydrophobic SAS of ligands decrease and
reach stable value. Hydrophilic remains stable over the simulation
time. I am wondering whether it  (the decrease o hydrophobic) is
because of binding to protein or aggregations of my small molecules
(They do aggregate) or both? I mean: how is it caculated? Is binding
to protein included in the decrease of the hydrophobic SAS of
lignads or it is impossible and  aggregation will be the one thing?
 
Thank you, 





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: g_sas of ligands

2011-09-09 Thread Steven Neumann
Was my question not clear or noone can help me? I am wondering whether
calculations of ligand hydrophobic SAS (decrease during the simualtion) can
be result of binding to protein?



On Fri, Sep 9, 2011 at 8:23 AM, Steven Neumann wrote:

> Dear Gromacs Users,
>
> I am calculating SAS using g_sas of ligands in my system: protein, 30
> ligands in water. The hydrophobic SAS of ligands decrease and reach stable
> value. Hydrophilic remains stable over the simulation time. I am wondering
> whether it  (the decrease o hydrophobic) is because of binding to protein or
> aggregations of my small molecules (They do aggregate) or both? I mean: how
> is it caculated? Is binding to protein included in the decrease of the
> hydrophobic SAS of lignads or it is impossible and  aggregation will be the
> one thing?
>
> Thank you,
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[gmx-users] atom type OXT

2011-09-09 Thread chris . neale
You still haven't provided all of the relevant information. For  
example: what ff are you using? But please don't just sent that  
information now... better for you to read about how to develop a good  
post and next time be suer to include enough information that we could  
reproduce the problem if we tried.


In any event, the OXT atom is not recognized by your force field.  
Depending on how many oxygen atoms you have in your final LEU residue,  
you should rename it as you see based on either ff*.rtp or ff*-c.tdb.  
I would personally keep only a single oxygen in your c-term LEU and  
rename it "O". You can add back the original coordinates by hand to  
the .gro if you wish. I am not sure if pdb2gmx can handle being  
supplied with the coordinates of the heavy atoms for the termini or  
not. In any event, this will let pdb2gmx produce the .top/.itp for you.


I am a little surprised that you are running into this because  
xlateat.dat should allow renaming of OXT --> O automatically but  
perhaps the problem is that you are supplying both O and OXT? (but  
then again you didn't provide the coordinates of the c-terminal  
residue).


To be honest I have not struggled with this much because I have always  
just done as I suggested to you above and it works fine. I guess it's  
possible that you are using a very old version of gromacs (but then  
again you didn't say what version you are using).


Chris.



Message: 4
Date: Tue, 06 Sep 2011 22:35:09 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] atom type OXT
To: Discussion list for GROMACS users 
Message-ID: <4E66137D.9040103 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 6/09/2011 11:39 AM, Sweta Iyer wrote:

Hi all,

I have been trying to pdbgmx my protein to obtain the gro and top files
as follows:

pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top -ter  -ignh

However, I get an error message that states:

Atom OXT in residue SER 29 was not found in rtp entry SER with 8 atoms
while sorting atoms


We don't know what termini you are choosing (or want), so it's hard to
help. See also
http://www.gromacs.org/Documentation/How-tos/Multiple_Chains

Mark



Hi,

I chose NH3+ as the start terminus at the first residue which is leucine
and COO- as my end terminus which is also on a leucine residue, which is
when it says it cant recognize atom type OXT on my last leucine residue.



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Re: [gmx-users] md.mdp file GPU one

2011-09-09 Thread Justin A. Lemkul



lina wrote:

Hi,


are there someone love to share one md.mdp file for GPU version?



All the details are here:

http://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=gpu

The benchmark archive has example .mdp files that you can tweak.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] md.mdp file GPU one

2011-09-09 Thread lina
Hi,


are there someone love to share one md.mdp file for GPU version?


Thanks ahead,

-- 
Best Regards,

lina
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[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

2011-09-09 Thread Marcin Zielinski

Ok, giving -DGMX_ACCELERATE=Power6 results with:

src/config.h
/* Define to a macro mangling the given C identifier (in lower and upper
   case), which must not contain underscores, for linking with Fortran. */
#define F77_FUNC(name,NAME)  name ##

/* As F77_FUNC, but for C identifiers containing underscores. */
#define F77_FUNC_(name,NAME) name ##

which, after issuing make, results with an error message at the very 
beginning:
"/home/grmcs454/gromacsdir/test-build/src/config.h", line 45.39: 
1506-210 (S) The ## operator requires two operands.
"/home/grmcs454/gromacsdir/test-build/src/config.h", line 48.39: 
1506-210 (S) The ## operator requires two operands.


I checked cmake/CMakeLists.txt and '##' are put explicitly therefor they 
will be present with _
afterwards or without it, thus giving this error every time You put 
Power6 or Fortran option on.

As far as I understand.


Only mdrun takes advantage of parallelism in GROMACS up to now. So the
non-threads requirement is moot for a build focused on the tools.

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Re: [gmx-users] Groamacs for metal ion

2011-09-09 Thread Mark Abraham
 
 
On 09/09/11, om prakash  wrote:

> 
> Dear friends
>  
> I am trying to gromacs simulation with the metal (Zn) binding protein. But 
> here, i am not able to make itp file for the metal..I am preety new to this 
> field...anyone please suggest me, what i should do?
> 

 
You should endeavour to use the same solution that someone else has already 
published on a similar protein. Preferably, read about several attempts and 
choose what looks like it works best. The details will vary with the form of 
the solution. 
 
Mark
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Re: [gmx-users] dialanine using charmm27 ff

2011-09-09 Thread Mark Abraham
 
 
On 09/09/11, Sandeep Somani  wrote:

> Hi Mark 
> 
> 
> Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and 
> renamed residue and atom names in pdb file. 
> 
> 
> But pdb2gmx is still complaining about the terminal groups. It seems to have 
> picked up ACE, but not CT3. 
> pdb2gmx error message and modified pdb file are listed below. Any idea ? Do I 
> need to modify .c.tdb ? If so, do you have that entry as well :) ? 
> 

 
Ah, no. To get rid of the warning, you need to teach GROMACS that CT3 is a 
protein residue. (It knew about ACE from other force fields.) Copy 
residuetypes.dat from the share/top directory to your working directory, and 
add CT3 as Protein at the end.
 
To get rid of the error, you need to tell pdb2gmx not to try to change your 
termini. Use pdb2gmx -ter, and choose "None" for both N and C termini.
 
Mark 

> 
> 
>  
> 
> 
> Thanks 
> Sandeep 
> 
> 
> =pdb2gmx error===
> 
> Back Off! I just backed up topol.top to ./#topol.top.3#
> Processing chain 1 (32 atoms, 4 residues)
> There are 3 donors and 3 acceptors
> There are 4 hydrogen bonds
> Identified residue ACE1 as a starting terminus.
> Warning: Residue CT32 in chain has different type (Other) from starting 
> residue ACE1 (Protein).
> Identified residue ALA2 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Start terminus ACE-1: NH3+
> End terminus ALA-2: COO-
> 
> 
> ---
> Program pdb2gmx_d, VERSION 4.5.4
> Source code file: pdb2top.c, line: 1070
> 
> 
> Fatal error:
> atom N not found in buiding block 1ACE while combining tdb and rtp
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> pdb2gmx error
> 
> 
> modified pdb=
> 
> 
> REMARK  NONE *
> 
> REMARK   DATE: 8/10/11  5:30:23  CREATED BY USER: ss2029  
> 
> ATOM  1  CT3 ACE 1  -2.160   0.537   0.930  1.00  0.00  DIAL
> ATOM  2  HT1 ACE 1  -2.466   0.003   0.005  1.00  0.00  DIAL
> ATOM  3  HT2 ACE 1  -2.562   1.572   0.910  1.00  0.00  DIAL
> ATOM  4  HT3 ACE 1  -2.562   0.001   1.816  1.00  0.00  DIAL
> ATOM  5  C   ACE 1  -0.672   0.582   1.009  1.00  0.00  DIAL
> ATOM  6  O   ACE 1  -0.105   1.128   1.954  1.00  0.00  DIAL
> ATOM  7  N   ALA 1   0.000   0.000   0.000  1.00  0.00  DIAL
> ATOM  8  HN  ALA 1  -0.453  -0.444  -0.769  1.00  0.00  DIAL
> ATOM  9  CA  ALA 1   1.459   0.000   0.000  1.00  0.00  DIAL
> ATOM 10  HA  ALA 1   1.812  -0.497   0.897  1.00  0.00  DIAL
> ATOM 11  CB  ALA 1   1.949  -0.834  -1.207  1.00  0.00  DIAL
> ATOM 12  HB1 ALA 1   1.514  -1.854  -1.155  1.00  0.00  DIAL
> ATOM 13  HB2 ALA 1   1.628  -0.373  -2.167  1.00  0.00  DIAL
> ATOM 14  HB3 ALA 1   3.056  -0.932  -1.214  1.00  0.00  DIAL
> ATOM 15  C   ALA 1   2.096   1.401   0.000  1.00  0.00  DIAL
> ATOM 16  O   ALA 1   1.425   2.432   0.000  1.00  0.00  DIAL
> ATOM 17  N   ALA 2   3.451   1.458   0.000  1.00  0.00  DIAL
> ATOM 18  HN  ALA 2   3.954   0.594   0.000  1.00  0.00  DIAL
> ATOM 19  CA  ALA 2   4.276   2.664   0.000  1.00  0.00  DIAL
> ATOM 20  HA  ALA 2   4.065   3.236  -0.897  1.00  0.00  DIAL
> ATOM 21  CB  ALA 2   3.864   3.539   1.207  1.00  0.00  DIAL
> ATOM 22  HB1 ALA 2   2.776   3.756   1.155  1.00  0.00  DIAL
> ATOM 23  HB2 ALA 2   4.063   3.014   2.167  1.00  0.00  DIAL
> ATOM 24  HB3 ALA 2   4.407   4.508   1.214  1.00  0.00  DIAL
> ATOM 25  C   ALA 2   5.791   2.399   0.000  1.00  0.00  DIAL
> ATOM 26  O   ALA 2   6.597   3.328   0.000  1.00  0.00  DIAL
> ATOM 27  N   CT3 2   6.175   1.110   0.000  1.00  0.00  DIAL
> ATOM 28  HN  CT3 2   5.528   0.351   0.000  1.00  0.00  DIAL
> ATOM 29  CT  CT3 2   7.566   0.777   0.000  1.00  0.00  DIAL
> ATOM 30  HT1 CT3 2   8.048   1.201   0.907  1.00  0.00  DIAL
> 
> 
> ATOM 31  HT2 CT3 2   7.683  -0.327   0.000  1.00  0.00  DIAL
> ATOM 32  HT3 CT3 2   8.048   1.201  -0.907  1.00  0.00  DIAL
> TER  33  CT3  2
> END
> 
> modified pdb=
> 
> 
> 
> 
> 
> 
> 
> 
> On Fri, Sep 9, 2011 at 2:52 AM, Mark Abraham  wrote:
> 
> 
> > 
> > On 9/09/2011 8:05 AM, Sandeep Somani wrot

[gmx-users] Groamacs for metal ion

2011-09-09 Thread om prakash
Dear friends

I am trying to gromacs simulation with the metal (Zn) binding protein. But
here, i am not able to make itp file for the metal..I am preety new to this
field...anyone please suggest me, what i should do?

-- 
Om Prakash Sharma
Ph.D Scholar & DIT JRF
Centre for Bioinformatics
Pondicherry University
Pondicherry-605014
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Re: [gmx-users] dialanine using charmm27 ff

2011-09-09 Thread Sandeep Somani
Hi Mark

Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and
renamed residue and atom names in pdb file.

But pdb2gmx is still complaining about the terminal groups. It seems to have
picked up ACE, but not CT3.
pdb2gmx error message and modified pdb file are listed below. Any idea ? Do
I need to modify .c.tdb ? If so, do you have that entry as well :) ?

Thanks
Sandeep

=pdb2gmx error===
Back Off! I just backed up topol.top to ./#topol.top.3#
Processing chain 1 (32 atoms, 4 residues)
There are 3 donors and 3 acceptors
There are 4 hydrogen bonds
Identified residue ACE1 as a starting terminus.
Warning: Residue CT32 in chain has different type (Other) from starting
residue ACE1 (Protein).
Identified residue ALA2 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ACE-1: NH3+
End terminus ALA-2: COO-

---
Program pdb2gmx_d, VERSION 4.5.4
Source code file: pdb2top.c, line: 1070

Fatal error:
atom N not found in buiding block 1ACE while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
pdb2gmx error

modified pdb=
REMARK  NONE *

REMARK   DATE: 8/10/11  5:30:23  CREATED BY USER: ss2029

*ATOM  1  CT3 ACE 1  -2.160   0.537   0.930  1.00  0.00
 DIAL*
*ATOM  2  HT1 ACE 1  -2.466   0.003   0.005  1.00  0.00
 DIAL*
*ATOM  3  HT2 ACE 1  -2.562   1.572   0.910  1.00  0.00
 DIAL*
*ATOM  4  HT3 ACE 1  -2.562   0.001   1.816  1.00  0.00
 DIAL*
*ATOM  5  C   ACE 1  -0.672   0.582   1.009  1.00  0.00
 DIAL*
*ATOM  6  O   ACE 1  -0.105   1.128   1.954  1.00  0.00
 DIAL*
ATOM  7  N   ALA 1   0.000   0.000   0.000  1.00  0.00  DIAL
ATOM  8  HN  ALA 1  -0.453  -0.444  -0.769  1.00  0.00  DIAL
ATOM  9  CA  ALA 1   1.459   0.000   0.000  1.00  0.00  DIAL
ATOM 10  HA  ALA 1   1.812  -0.497   0.897  1.00  0.00  DIAL
ATOM 11  CB  ALA 1   1.949  -0.834  -1.207  1.00  0.00  DIAL
ATOM 12  HB1 ALA 1   1.514  -1.854  -1.155  1.00  0.00  DIAL
ATOM 13  HB2 ALA 1   1.628  -0.373  -2.167  1.00  0.00  DIAL
ATOM 14  HB3 ALA 1   3.056  -0.932  -1.214  1.00  0.00  DIAL
ATOM 15  C   ALA 1   2.096   1.401   0.000  1.00  0.00  DIAL
ATOM 16  O   ALA 1   1.425   2.432   0.000  1.00  0.00  DIAL
ATOM 17  N   ALA 2   3.451   1.458   0.000  1.00  0.00  DIAL
ATOM 18  HN  ALA 2   3.954   0.594   0.000  1.00  0.00  DIAL
ATOM 19  CA  ALA 2   4.276   2.664   0.000  1.00  0.00  DIAL
ATOM 20  HA  ALA 2   4.065   3.236  -0.897  1.00  0.00  DIAL
ATOM 21  CB  ALA 2   3.864   3.539   1.207  1.00  0.00  DIAL
ATOM 22  HB1 ALA 2   2.776   3.756   1.155  1.00  0.00  DIAL
ATOM 23  HB2 ALA 2   4.063   3.014   2.167  1.00  0.00  DIAL
ATOM 24  HB3 ALA 2   4.407   4.508   1.214  1.00  0.00  DIAL
ATOM 25  C   ALA 2   5.791   2.399   0.000  1.00  0.00  DIAL
ATOM 26  O   ALA 2   6.597   3.328   0.000  1.00  0.00  DIAL
*ATOM 27  N   CT3 2   6.175   1.110   0.000  1.00  0.00
 DIAL*
*ATOM 28  HN  CT3 2   5.528   0.351   0.000  1.00  0.00
 DIAL*
*ATOM 29  CT  CT3 2   7.566   0.777   0.000  1.00  0.00
 DIAL*
*ATOM 30  HT1 CT3 2   8.048   1.201   0.907  1.00  0.00
 DIAL*
*ATOM 31  HT2 CT3 2   7.683  -0.327   0.000  1.00  0.00
 DIAL*
*ATOM 32  HT3 CT3 2   8.048   1.201  -0.907  1.00  0.00
 DIAL*
TER  33  CT3  2
END
modified pdb=




On Fri, Sep 9, 2011 at 2:52 AM, Mark Abraham wrote:

> On 9/09/2011 8:05 AM, Sandeep Somani wrote:
>
>> Hi
>>
>> I am trying to set up a simulation for dialanine using charmm27 ff but am
>> getting errors in pdb2gmx due to missing definitions in rtp file.
>>
>> I created the pdb file (below) using Charmm for the sequence
>> ACE-ALA-ALA-CT3.
>>
>> pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE and
>> CT3.
>>
>
> Yes, CHARMM in GROMACS has lacked these for some time. I asked over a year
> ago for them to be added, but that hasn't happened. You can add
>
> [ ACE ]
>  [ atoms ]
>CT3 CT3 -0.270  0
>HT1 HA  0.090   1
>HT2 HA  0.090   2
>HT3 HA  0.090   3
>C   C   0.510   4
>O   O   -0.510  5
>  [ bonds ]
>C   CT3
>C   +N
>CT3 HT31
>CT3 HT32
>   

Re: [gmx-users] amb2gmx.pl to convert GLYCAM topology

2011-09-09 Thread Alan
Or why not trying acpype?

Cheers,

Alan

On 9 September 2011 07:37, Mark Abraham  wrote:

>  On 9/09/2011 4:21 PM, Yun Shi wrote:
>
> Hi all,
>
> I understand this problem has been discussed before, but it seems no
> conclusion has been drawn.
>
>
> Someone needs to do some work and report back :-)
>
>
>
> GLYCAM force field assigns negative force constants to some dihedrals, and
> when amb2gmx.pl was used to convert prmtop file to gromacs top file, these
> negative values seem to be ignored. Some people proposed that we change the
> code in amb2gmx.pl, that is:
>
> ...
>
>   # get all force constants for each line of a dihedral #
>   my $lines = $i -1 +$numijkl;
>   for(my $j=$i;$j<=$lines;$j++){
> my $period = abs($pn{$j});
> if($pk{$j}>0) {
>   $V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
> }
>
> ...
>
> the "$pk{$j}>0" is modified to "$pk{$j}!=0".
>
> Others suggest to modify the original prmtop file, that is, to remove the
> negative signs, and correspondingly, change the phase shift from 0 to 180.
> Then amb2gmx.pl could be used to correctly convert the topology.
>
> I am wondering if the first approach has been validated, since the second
> one seems complicated and laborious to carry out.
>
>
> Seems like a straightforward job for regular expression replacement using
> sed/perl/python/whatever. It might even be a one-liner.
>
> Mark
>
> --
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>



-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

2011-09-09 Thread Mark Abraham

On 9/09/2011 5:50 PM, Marcin Zielinski wrote:

Hi Mark,

Yes, GMX_ACCELERATION should do the trick, however it requires You to 
turn off the THREADS.
Altho ppl tend to run the tools in serial anyway, I somehow sticked to 
that.


Only mdrun takes advantage of parallelism in GROMACS up to now. So the 
non-threads requirement is moot for a build focused on the tools.




As for the FindLAPACK.cmake fix, I'm pretty sure I has been posted 
here some time ago. I googled it

anyhow.

Would be handy If I could put my hands on some benchmarking suit so 
that I could test this given
setup on my own and compare it to the build with POWER6 included (and 
without THREADS). Should I

see some boost in the speed in execution time?


Probably nothing much. There is no up-to-date benchmark suite.

Mark
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[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

2011-09-09 Thread Marcin Zielinski

Hi Mark,

Yes, GMX_ACCELERATION should do the trick, however it requires You to 
turn off the THREADS.

Altho ppl tend to run the tools in serial anyway, I somehow sticked to that.

As for the FindLAPACK.cmake fix, I'm pretty sure I has been posted here 
some time ago. I googled it

anyhow.

Would be handy If I could put my hands on some benchmarking suit so that 
I could test this given
setup on my own and compare it to the build with POWER6 included (and 
without THREADS). Should I

see some boost in the speed in execution time?

best regards,
--
Marcin Zielinski
Supercomputing group, OSD
SARA
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Re: [gmx-users] gridcount

2011-09-09 Thread Mark Abraham

On 9/09/2011 5:27 PM, aiswarya pawar wrote:

Hi all,

am facing an error while installing gridcount-

make[1]: *** [g_ri3Dc.o] Error 1
make[1]: Leaving directory `/home/proj11/aiswarya/Grid-count/src'
make: *** [all] Error 2

This error is while giving the make command.


This is not the right forum for this question, and when you do submit to 
the right forum, they will want to see considerably more of the output.


Mark
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[gmx-users] gridcount

2011-09-09 Thread aiswarya pawar
Hi all,

am facing an error while installing gridcount-

make[1]: *** [g_ri3Dc.o] Error 1
make[1]: Leaving directory `/home/proj11/aiswarya/Grid-count/src'
make: *** [all] Error 2

This error is while giving the make command.

Thanks
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[gmx-users] g_sas of ligands

2011-09-09 Thread Steven Neumann
Dear Gromacs Users,

I am calculating SAS using g_sas of ligands in my system: protein, 30
ligands in water. The hydrophobic SAS of ligands decrease and reach stable
value. Hydrophilic remains stable over the simulation time. I am wondering
whether it  (the decrease o hydrophobic) is because of binding to protein or
aggregations of my small molecules (They do aggregate) or both? I mean: how
is it caculated? Is binding to protein included in the decrease of the
hydrophobic SAS of lignads or it is impossible and  aggregation will be the
one thing?

Thank you,
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