Re: [gmx-users] multiple ligands topology

[Jennifer Vo]

Dear Justin,
Many thanks again. I just define a small box then insert molecules and let
it floating nearby the protein, then redefine the actual box for the real
concentration of protein.
The maxwarn 27 is from this
"NOTE 1 [file em_ion.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.
Setting the LD random seed to 2002995045
WARNING 1 [file my_ligand_atomtypes.itp, line 3]:
  Overriding atomtype CA

WARNING 2 [file my_ligand_atomtypes.itp, line 4]:
  Overriding atomtype H4

WARNING 3 [file my_ligand_atomtypes.itp, line 5]:
  Overriding atomtype HA

WARNING 4 [file my_ligand_atomtypes.itp, line 6]:
  Overriding atomtype C

WARNING 5 [file my_ligand_atomtypes.itp, line 7]:
  Overriding atomtype O

WARNING 6 [file my_ligand_atomtypes.itp, line 8]:
  Overriding atomtype N

WARNING 7 [file my_ligand_atomtypes.itp, line 9]:
  Overriding atomtype H

WARNING 8 [file my_ligand_atomtypes.itp, line 10]:
  Overriding atomtype N*

WARNING 9 [file my_ligand_atomtypes.itp, line 11]:
  Overriding atomtype CT

WARNING 10 [file my_ligand_atomtypes.itp, line 12]:
  Overriding atomtype H2

WARNING 11 [file my_ligand_atomtypes.itp, line 13]:
  Overriding atomtype H1

WARNING 12 [file my_ligand_atomtypes.itp, line 14]:
  Overriding atomtype OH

WARNING 13 [file my_ligand_atomtypes.itp, line 15]:
  Overriding atomtype HO

WARNING 14 [file my_ligand_atomtypes.itp, line 16]:
  Overriding atomtype OS

WARNING 15 [file my_ligand_atomtypes.itp, line 17]:
  Overriding atomtype P

WARNING 16 [file my_ligand_atomtypes.itp, line 18]:
  Overriding atomtype O2

WARNING 17 [file my_ligand_atomtypes.itp, line 19]:
  Overriding atomtype CK

WARNING 18 [file my_ligand_atomtypes.itp, line 20]:
  Overriding atomtype H5

WARNING 19 [file my_ligand_atomtypes.itp, line 21]:
  Overriding atomtype NB

WARNING 20 [file my_ligand_atomtypes.itp, line 22]:
  Overriding atomtype CB

WARNING 21 [file my_ligand_atomtypes.itp, line 23]:
  Overriding atomtype N2

WARNING 22 [file my_ligand_atomtypes.itp, line 24]:
  Overriding atomtype NC

WARNING 23 [file my_ligand_atomtypes.itp, line 25]:
  Overriding atomtype CQ
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'A'
Excluding 3 bonded neighbours molecule type 'B'
Excluding 3 bonded neighbours molecule type 'NPD'
Excluding 3 bonded neighbours molecule type 'IR3'
Excluding 2 bonded neighbours molecule type 'SOL'
"
And I think it's harmless to ignore the warning here for the overriding
atomtype. Am I correct? The image of ligand is in the link
http://postimg.org/image/fojbmkhrb/
I would really appreciate for a help.
Regards,
Jennifer
On Fri, Feb 13, 2015 at 10:45 PM, Justin Lemkul  wrote:

>
>
> On 2/13/15 2:47 PM, Jennifer Vo wrote:
>
>> Dear Justin,
>> Please find the figure of output pdb file after minimizatrion.(I have sent
>> in the previous email but it's pending... So I send it again)
>>
>>
> The list doesn't accept attachments (if I had a nickel for every time I
> said that...) so if you want to share images, upload them to a file-sharing
> service and post the URL.
>
>  Here is step by step how I built the system
>> ### concatenate 2 chains and renumber the residues
>> genconf -f AB.gro -o AB_renumber.gro -renumber
>> ### redefine the small box the the proteins
>> editconf -f AB_renumber.gro -o AB_box.gro -bt cubic -d 0.5 -c
>> ### insert the first ligand
>> gmx insert-molecules -f AB_box.gro  -ci  ligand1.gro -o AB_NADPH.pdb
>> -nmol 1
>> ### insert the second ligand
>> gmx insert-molecules -f AB_NADPH.pdb  -ci  ir3_em.gro -o AB_NADPH_IR3.pdb
>> -nmol 9 -seed -1
>>
>
> OK, so "ligands" are actually just randomly inserted molecules, freely
> floating in the solvent.
>
>  ### redefine the box the the system
>> editconf -f AB_NADPH_IR3.pdb -o AB_NADPH_IR3_box.pdb -bt cubic -d 1.0 -c
>>
>
> Why is this necessary?
>
>  ### adding water
>> gmx solvate -cp AB_NADPH_IR3_box.pdb -cs spc216.gro -o
>> AB_NADPH_IR3_solvate.pdb -p topol.top
>> ### convert pdb to gro file
>> editconf -f AB_NADPH_IR3_solvate.pdb -o AB_NADPH_IR3_solvate.gro
>> ### adding ions
>> grompp -f em_ion.mdp -c AB_NADPH_IR3_solvate.gro -p topol.top -o ions.tpr
>> -maxwarn 27
>>
>
> The use of -maxwarn 27 is alarming.  Why are you trying to override 27
> errors? This would be suspect #1 in diagnosing problems.
>
> -Justin
>
>
>  genion -s ions.tpr -o AB_NADPH_IR3_solvate_ions.gro -p topol.top -pname NA
>> -np 24 -n index.ndx
>>
>> Many thanks for your help.
>>
>> On Fri, Feb 13, 2015 at 4:01 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 2/13/15 9:59 AM, Jennifer Vo wrote:
>>>
>>>  Dear Justin,
 Many thanks for your kind answer. The output of minimization for
 Protein +
 1 Ligand
 Steepest Descents converged to Fmax < 100 in 868 steps
 Potential Energy  = -8.040

[gmx-users] breaking S-S bond using pdb2gmx

[Sahithya S Iyer]

Deal all,
I need to break 1 out of 4 S-S bonds in a protein. While using the pdb2gmx
command, i used -ss whereby i was asked which S-S bonds i would what to
keep intact and which i'd break. Since i wanted the S-S bond between CYS
6-CYS 127 to be broken, i gave he following command -
Link CYS-6 SG-48 and CYS-127 SG-981 (y/n) ?n
Link CYS-30 SG-238 and CYS-115 SG-889 (y/n) ?y
Link CYS-64 SG-513 and CYS-80 SG-630 (y/n) ?y
Link CYS-76 SG-601 and CYS-94 SG-724 (y/n) ?y
The .gro file generated , visualised using vmd, shows 4 S-S bonds instead
of 3. Where have i gone wrong. Is there any other method the break the S-S
bonds present in the pdb file ?
Thanks in advance.

-- 
Sahithya S Iyer
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[gmx-users] GPU Installation

[Carmen Di Giovanni]

Dear all,
I would like to known if Gromacs can be installed on 8 GPU GTX Titan in parallel
Thank you in advance
Carmen 



Carmen Di Giovanni, PhD
Postdoctoral Researcher
Dept. of Pharmacy
"Drug Discovery Lab"
University of Naples "Federico II"
Via D. Montesano, 49
80131 Naples
Tel.: ++39 081 678623
Fax: ++39 081 678100
Email: cdigi...@unina.it
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Re: [gmx-users] lower Area per lipid for DPPC with CHARMM36

[tarak karmakar]

Oh! Thanks. :)
Sorry I should have checked it before running the simulation.
Now, I'm getting APL ~62.5 A^2 which is pretty good compared to the expt.


On Sun, Feb 15, 2015 at 6:28 PM, Justin Lemkul  wrote:

>
>
> On 2/15/15 7:39 AM, tarak karmakar wrote:
>
>> Dear All,
>> All atom simulation of DPPC bilayer (128 lipids) is resulting a low area
>> per lipid (sliding down from ~58 to ~54 in 4 ns NPT).
>> I'm performing the simulation in gromacs-5.0.4 with the charmm36 force
>> field parameters for the lipid molecules. The NPT.mdp is pasted bellow,
>>
>>
> We've been discussing this exact topic in another thread for days...
>
> Your .mdp settings are wrong.
>
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> -Justin
>
>
>  
>> -
>> title= NPT production for cxcr_WT
>> ; Parameters describing the details of the NVT simulation protocol
>> integrator= md; Algorithm ("md" = molecular dynamics
>> [leap-frog
>> integrator]; "md-vv" = md using velocity verlet; sd = stochastic dynamics)
>> dt= 0.002; Time-step (ps)
>> nsteps= 500; Number of steps to run (0.002 * 50 = 1
>> ns)
>>
>> ; Parameters controlling output writing
>> nstxout= 1; Write coordinates to output .trr file
>> every
>> 2 ps
>> nstvout= 1; Write velocities to output .trr file every
>> 2 ps
>> nstenergy= 1; Write energies to output .edr file every 2
>> ps
>> nstlog= 1; Write output to .log file every 2 ps
>>
>> ; Parameters describing neighbors searching and details about interaction
>> calculations
>> ns_type= grid; Neighbor list search method (simple, grid)
>> nstlist= 5; Neighbor list update frequency (after every
>> given number of steps)
>> rlist= 1.2; Neighbor list search cut-off distance (nm)
>> rlistlong   = 1.4
>>
>> rcoulomb = 1.2   ; short-range electrostatic cutoff
>> (in
>> nm)
>>
>> vdwtype  = switch
>> rvdw = 1.2   ; short-range van der Waals cutoff
>> (in
>> nm)
>> rvdw_switch  = 0.8
>>
>> pbc= xyz; Direction in which to use Perodic Boundary
>> Conditions (xyz, xy, no)
>>
>> ; Parameters for treating bonded interactions
>> continuation= no; Whether a fresh start or a continuation from
>> a previous run (yes/no)
>> constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE)
>> constraints= all-bonds; Which bonds/angles to constrain (all-bonds
>> / hbonds / none / all-angles / h-angles)
>> lincs_iter= 1; Number of iterations to correct for rotational
>> lengthening in LINCS (related to accuracy)
>> lincs_order= 4; Highest order in the expansion of the
>> constraint coupling matrix (related to accuracy)
>>
>> ; Parameters for treating electrostatic interactions
>> coulombtype= PME; Long range electrostatic interactions
>> treatment (cut-off, Ewald, PME)
>> pme_order= 4; Interpolation order for PME (cubic interpolation
>> is represented by 4)
>> fourierspacing= 0.16; Maximum grid spacing for FFT grid using
>> PME (nm)
>>
>> ; Temperature coupling parameters
>> tcoupl= Nose-Hoover; Modified Berendsen thermostat
>> using velocity rescaling
>> tc-grps= DPPC SOL_Ion; Define groups to be coupled separately
>> to temperature bath
>> tau_t= 0.50.5; Group-wise coupling time constant (ps)
>> ref_t= 300300; Group-wise reference temperature (K)
>>
>> ; Pressure coupling parameters
>> pcoupl= Parrinello-Rahman; Pressure coupler used under NPT
>> conditions
>> pcoupltype= semiisotropic; Isotropic scaling in the x-y
>> direction, independent of the z direction
>> tau_p= 5.0; Coupling time constant (ps)
>> ref_p= 1.01.0; Reference pressure for coupling,
>> x-y, z directions (bar)
>> compressibility = 4.5e-54.5e-5; Isothermal compressibility
>> (bar^-1)
>>
>> ; Miscellaneous control parameters
>> ; Dispersion correction
>> DispCorr= EnerPres; Dispersion corrections for Energy and
>> Pressure for vdW cut-off
>> ; Initial Velocity Generation
>> gen_vel= no; Velocity is read from the previous run
>> ; Centre of mass (COM) motion removal relative to the specified groups
>> nstcomm= 1; COM removal frequency (steps)
>> comm_mode= Linear; Remove COM translation (linear / angular /
>> no)
>> comm_grps= DPPC SOL_Ion; COM removal relative to the specified
>> groups
>> 
>> ---
>> Any suggestions would be appreciated.
>>
>> Thanks,
>> Tarak
>>
>>
> --
> =

Re: [gmx-users] GPU Installation

[Mark Abraham]

Hi,

Technically yes, but usefully, no. I suspect all GPU MD implementation need
several tens of thousands of particles per GPU to work efficiently, and the
more GPUs the more issues there are to manage (for software and hardware).
The GROMACS implementation needs a comparably tasty CPU, which you probably
can't get for 8 GTX Titans. So for GROMACS, I would think more in terms of
4 Titans per dual-socket Haswell node.

Mark

On Mon, Feb 16, 2015 at 11:30 AM, Carmen Di Giovanni 
wrote:

> Dear all,
> I would like to known if Gromacs can be installed on 8 GPU GTX Titan in
> parallel
> Thank you in advance
> Carmen
>
>
>
> Carmen Di Giovanni, PhD
> Postdoctoral Researcher
> Dept. of Pharmacy
> "Drug Discovery Lab"
> University of Naples "Federico II"
> Via D. Montesano, 49
> 80131 Naples
> Tel.: ++39 081 678623
> Fax: ++39 081 678100
> Email: cdigi...@unina.it
> --
> 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.
>
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Re: [gmx-users] Re; calculating interaction energies of dimers and ligand

[Justin Lemkul]

On 2/16/15 12:03 AM, RJ wrote:

Dear Justin,


I notice that -rerun option in mdrun.


As per your suggestion, i have made a tpr file using energyrps in md.mdp file 
as like this




gmx grompp -f md.mdp -c npt.gro -t npt.cpt -o check.tpr




and tried to use mdrun -reun




gmx mdrun -rerun check


but end up with


Can not open file:
topol.tpr



Right, because mdrun always needs instructions for what to actually do.  You 
make a new .tpr file with whatever groups you want for interaction energy, and 
use mdrun -rerun to calculate those quantities.


-Justin







Dear Justin,


I already ran 10 ns without mentioned the energyrps. Now I have added the 
energyrps in md.mdp file. Should i need to rerun 10 ns again to get the 
interaction energies?


what does mdrun -rerun ?
On 2/13/15 7:07 AM, RJ wrote:

Dear all,


I need to calculate the interaction energy (Column SR & LJ SR) of chain A with 
chain B.


Should I need to select the specific interacting residues to between chain A 
and B ? Also to chain C ( Ligand molecule)?. I used the gmx energy command line 
but there are index.ndx option to indicate the group of residues so?



To get this information printed to the .edr file, you need to do your run with
correct energygrps defined. If you didn't do that, create a .tpr file that
specifies these groups and re-calculate energies with mdrun -rerun.



Also, how do i calculate the interaction energies in nano second time scale ( 
seems there is no -tu option in gmx energy)?



Just convert after the fact in the text file or plotting software. The time
unit is always ps in .edr files.

-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] breaking S-S bond using pdb2gmx

[Justin Lemkul]

On 2/16/15 4:27 AM, Sahithya S Iyer wrote:

Deal all,
I need to break 1 out of 4 S-S bonds in a protein. While using the pdb2gmx
command, i used -ss whereby i was asked which S-S bonds i would what to
keep intact and which i'd break. Since i wanted the S-S bond between CYS
6-CYS 127 to be broken, i gave he following command -
Link CYS-6 SG-48 and CYS-127 SG-981 (y/n) ?n
Link CYS-30 SG-238 and CYS-115 SG-889 (y/n) ?y
Link CYS-64 SG-513 and CYS-80 SG-630 (y/n) ?y
Link CYS-76 SG-601 and CYS-94 SG-724 (y/n) ?y
The .gro file generated , visualised using vmd, shows 4 S-S bonds instead
of 3. Where have i gone wrong. Is there any other method the break the S-S
bonds present in the pdb file ?


The topology is definitive, not what you see in VMD.  Though the -SH groups 
should be obviously present.  Make sure you're visualizing the right file.


-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] multiple ligands topology

[Justin Lemkul]

On 2/16/15 3:49 AM, Jennifer Vo wrote:

Dear Justin,
Many thanks again. I just define a small box then insert molecules and let
it floating nearby the protein, then redefine the actual box for the real
concentration of protein.
The maxwarn 27 is from this
"NOTE 1 [file em_ion.mdp]:
   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
   that with the Verlet scheme, nstlist has no effect on the accuracy of
   your simulation.
Setting the LD random seed to 2002995045
WARNING 1 [file my_ligand_atomtypes.itp, line 3]:
   Overriding atomtype CA

WARNING 2 [file my_ligand_atomtypes.itp, line 4]:
   Overriding atomtype H4

WARNING 3 [file my_ligand_atomtypes.itp, line 5]:
   Overriding atomtype HA

WARNING 4 [file my_ligand_atomtypes.itp, line 6]:
   Overriding atomtype C

WARNING 5 [file my_ligand_atomtypes.itp, line 7]:
   Overriding atomtype O

WARNING 6 [file my_ligand_atomtypes.itp, line 8]:
   Overriding atomtype N

WARNING 7 [file my_ligand_atomtypes.itp, line 9]:
   Overriding atomtype H

WARNING 8 [file my_ligand_atomtypes.itp, line 10]:
   Overriding atomtype N*

WARNING 9 [file my_ligand_atomtypes.itp, line 11]:
   Overriding atomtype CT

WARNING 10 [file my_ligand_atomtypes.itp, line 12]:
   Overriding atomtype H2

WARNING 11 [file my_ligand_atomtypes.itp, line 13]:
   Overriding atomtype H1

WARNING 12 [file my_ligand_atomtypes.itp, line 14]:
   Overriding atomtype OH

WARNING 13 [file my_ligand_atomtypes.itp, line 15]:
   Overriding atomtype HO

WARNING 14 [file my_ligand_atomtypes.itp, line 16]:
   Overriding atomtype OS

WARNING 15 [file my_ligand_atomtypes.itp, line 17]:
   Overriding atomtype P

WARNING 16 [file my_ligand_atomtypes.itp, line 18]:
   Overriding atomtype O2

WARNING 17 [file my_ligand_atomtypes.itp, line 19]:
   Overriding atomtype CK

WARNING 18 [file my_ligand_atomtypes.itp, line 20]:
   Overriding atomtype H5

WARNING 19 [file my_ligand_atomtypes.itp, line 21]:
   Overriding atomtype NB

WARNING 20 [file my_ligand_atomtypes.itp, line 22]:
   Overriding atomtype CB

WARNING 21 [file my_ligand_atomtypes.itp, line 23]:
   Overriding atomtype N2

WARNING 22 [file my_ligand_atomtypes.itp, line 24]:
   Overriding atomtype NC

WARNING 23 [file my_ligand_atomtypes.itp, line 25]:
   Overriding atomtype CQ
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'A'
Excluding 3 bonded neighbours molecule type 'B'
Excluding 3 bonded neighbours molecule type 'NPD'
Excluding 3 bonded neighbours molecule type 'IR3'
Excluding 2 bonded neighbours molecule type 'SOL'
"
And I think it's harmless to ignore the warning here for the overriding
atomtype. Am I correct? The image of ligand is in the link


Well, if you're overriding atom types, that means you're potentially changing 
elements of the force field.  That can cause catastrophic problems if you're not 
careful.  If these types are simply re-defining the same parameters already in 
the force field, then yes it is safe, but also inherently unnecessary.



http://postimg.org/image/fojbmkhrb/


Some of these ligands have extremely bizarre geometries, with H overlapping 
heavy atoms.  Something looks very wrong.


-Justin


I would really appreciate for a help.
Regards,
Jennifer
On Fri, Feb 13, 2015 at 10:45 PM, Justin Lemkul  wrote:




On 2/13/15 2:47 PM, Jennifer Vo wrote:


Dear Justin,
Please find the figure of output pdb file after minimizatrion.(I have sent
in the previous email but it's pending... So I send it again)



The list doesn't accept attachments (if I had a nickel for every time I
said that...) so if you want to share images, upload them to a file-sharing
service and post the URL.

  Here is step by step how I built the system

### concatenate 2 chains and renumber the residues
genconf -f AB.gro -o AB_renumber.gro -renumber
### redefine the small box the the proteins
editconf -f AB_renumber.gro -o AB_box.gro -bt cubic -d 0.5 -c
### insert the first ligand
gmx insert-molecules -f AB_box.gro  -ci  ligand1.gro -o AB_NADPH.pdb
-nmol 1
### insert the second ligand
gmx insert-molecules -f AB_NADPH.pdb  -ci  ir3_em.gro -o AB_NADPH_IR3.pdb
-nmol 9 -seed -1



OK, so "ligands" are actually just randomly inserted molecules, freely
floating in the solvent.

  ### redefine the box the the system

editconf -f AB_NADPH_IR3.pdb -o AB_NADPH_IR3_box.pdb -bt cubic -d 1.0 -c



Why is this necessary?

  ### adding water

gmx solvate -cp AB_NADPH_IR3_box.pdb -cs spc216.gro -o
AB_NADPH_IR3_solvate.pdb -p topol.top
### convert pdb to gro file
editconf -f AB_NADPH_IR3_solvate.pdb -o AB_NADPH_IR3_solvate.gro
### adding ions
grompp -f em_ion.mdp -c AB_NADPH_IR3_solvate.gro -p topol.top -o ions.tpr
-maxwarn 27



The use of -maxwarn 27 is alarming.  Why are you trying to override 27
errors? This would be suspect #1 in diagnosing problems.

-Justin


  genion -s ions.tpr -o AB_NADPH_IR3_sol

Re: [gmx-users] Problem executing do_dssp in gromacs

[Justin Lemkul]

On 2/16/15 2:27 AM, Aarti rana wrote:

Hi Justin,

Yes, I have checked the env variables and file is also executable. But
still giving fatal error and asking me to specify the dssp version.



The error message is just generic, because most times the issue is an incorrect 
version.  You're sure your DSSP binary is 2.0.4?  What does 'echo $DSSP' return?


-Justin


Aarti



On Fri, Feb 13, 2015 at 8:13 PM, Justin Lemkul  wrote:




On 2/13/15 4:41 AM, Aarti rana wrote:


Hi,

I am new to gromacs and using gromacs 4.6.5 and dssp-2.0.4. To study the
secondary structure, when I am running these commands:

export DSSP=/usr/local/bin/dssp do_dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc
-o dssp.xvg -ver 2

I am getting this error:

dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a > /dev/null 2>
/dev/null' Reading frame 0 time 0.000 Back Off! I just backed up dd31ZWbc
to ./#dd31ZWbc.1#

---Program do_dssp,
VERSION 4.6.5 Source code file:
/build/buildd/gromacs-4.6.5/src/tools/gmx_do_dssp.c, line: 669

Fatal error: Failed to execute command: Try specifying your dssp version
with the -ver option.

I have already checked many helping sites but couldn't solve it. I have
also checked the earlier comments posted here.

I don't know how to fix it. Please help me?



Is your DSSP environment variable the correct location of the dssp binary
and is the dssp binary executable?

-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

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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

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Re: [gmx-users] GPU Installation

[Carmen Di Giovanni]

Many thanks Mark






- Original Message - 
From: "Mark Abraham" 

To: "Discussion list for GROMACS users" 
Sent: Monday, February 16, 2015 1:15 PM
Subject: Re: [gmx-users] GPU Installation



Hi,

Technically yes, but usefully, no. I suspect all GPU MD implementation 
need
several tens of thousands of particles per GPU to work efficiently, and 
the

more GPUs the more issues there are to manage (for software and hardware).
The GROMACS implementation needs a comparably tasty CPU, which you 
probably

can't get for 8 GTX Titans. So for GROMACS, I would think more in terms of
4 Titans per dual-socket Haswell node.

Mark

On Mon, Feb 16, 2015 at 11:30 AM, Carmen Di Giovanni 
wrote:


Dear all,
I would like to known if Gromacs can be installed on 8 GPU GTX Titan in
parallel
Thank you in advance
Carmen



Carmen Di Giovanni, PhD
Postdoctoral Researcher
Dept. of Pharmacy
"Drug Discovery Lab"
University of Naples "Federico II"
Via D. Montesano, 49
80131 Naples
Tel.: ++39 081 678623
Fax: ++39 081 678100
Email: cdigi...@unina.it
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Re: [gmx-users] breaking S-S bond using pdb2gmx

[Sahithya S Iyer]

Thanks for the reply Justin.

yes, i do notice the topology files have the S-H bonds.

On Mon, Feb 16, 2015 at 6:10 PM, Justin Lemkul  wrote:

>
>
> On 2/16/15 4:27 AM, Sahithya S Iyer wrote:
>
>> Deal all,
>> I need to break 1 out of 4 S-S bonds in a protein. While using the pdb2gmx
>> command, i used -ss whereby i was asked which S-S bonds i would what to
>> keep intact and which i'd break. Since i wanted the S-S bond between CYS
>> 6-CYS 127 to be broken, i gave he following command -
>> Link CYS-6 SG-48 and CYS-127 SG-981 (y/n) ?n
>> Link CYS-30 SG-238 and CYS-115 SG-889 (y/n) ?y
>> Link CYS-64 SG-513 and CYS-80 SG-630 (y/n) ?y
>> Link CYS-76 SG-601 and CYS-94 SG-724 (y/n) ?y
>> The .gro file generated , visualised using vmd, shows 4 S-S bonds instead
>> of 3. Where have i gone wrong. Is there any other method the break the S-S
>> bonds present in the pdb file ?
>>
>
> The topology is definitive, not what you see in VMD.  Though the -SH
> groups should be obviously present.  Make sure you're visualizing the right
> file.
>
> -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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-- 
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Re: [gmx-users] Regarding DSSP

[Justin Lemkul]

On 2/16/15 12:21 AM, HANNIBAL LECTER wrote:

Hello all:

I am not really sure, what are the various compatibility issues between the
do_dssp program of different Gromacs versions and the versions of the DSSP
program itself.

I am trying to use dssp 2.0.4 and Gromacs 4.5.6.

I have used

export DSSP=/usr/bin/dssp
and then do_dssp - 



The '...' part is the most important aspect of this problem report.  Always 
include full commands.



I am getting

Fatal error:
Failed to execute command: /usr/bin/dssp -na ddMjYR8P ddfm1ecX > /dev/null
2> /dev/null.



This is DSSP version 1 syntax.  The clue is -na; this means your do_dssp command 
is trying to use -ver 1 when it should be using -ver 2.


-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] Problem executing do_dssp in gromacs

[Justin Lemkul]

After looking at this a bit more closely for someone else who asked the same 
question, your clue is here:


dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a > /dev/null 2> /dev/null'

For some reason your do_dssp command is triggering version 1 syntax.  A version 
2 command should be something like:


dssp cmd='/usr/local/bin/dssp -i ddYB5REk -o ddxi1TAx > /dev/null 2> /dev/null'

Note the difference in -i/-o vs. -na.  This is the nature of the problem when 
dealing with different versions.  Somehow there's a disconnect between your DSSP 
version or the command you're telling us you're issuing.


-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
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Re: [gmx-users] Semiisotropic pressure coupling

[shivangi nangia]

Thanks a lot Justin!!!






On Sun, Feb 15, 2015 at 1:13 PM, Justin Lemkul  wrote:

>
>
> On 2/15/15 1:02 PM, shivangi nangia wrote:
>
>> Dear Justin,
>>
>> Thanks for the continuous help.
>>
>> Since I have done reverse CG, The CG POPC was equilibrated alone
>> anisotropically, The APL was fine there.
>> On reverse CG and NVT its still fine, it only after NPT it starts
>> dropping.
>>
>>
> Of course it's fine during NVT - the box can't change so the area is
> constant.
>
>  I am calculating APL as (2*Lx*Ly)/(No. of Lipids).
>>
>>
> That's only valid for pure, symmetric membranes.  You have a protein
> embedded in one leaflet, so this method is wrong.
>
>  You mentioned to get gull force field from your site, is it here:
>>
>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>>
>>
> Yes, that's the right place.
>
>  On unzipping this I see POPC is an .trp entry.
>>
>> If there is some other database, kindly point it out to me.
>>
>>
> What I'm telling you is to use those force field files to (1) verify that
> your POPC parameters are right (they should be) and (2) you'll have the
> right protein topology (there are different bonded parameters that will
> affect protein dynamics).
>
> Again, I must emphasize - troubleshooting the APL of this system with
> respect to the known APL of pure POPC is pointless.  You have a protein
> that convolutes (and potentially changes) everything.  If you want to
> simulate pure POPC to verify that things are fine, do that.  But taking
> more time on any perceived discrepancies here is not productive.
>
>
> -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] Regarding DSSP

[HANNIBAL LECTER]

Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is not
a scope to specify using the -ver command in this particular version as
opposed to the newer versions (5.0.4).

By '' I meant

do_dssp -f prot.xtc -s prot.tpr.

How do I specify a dssp version in gromacs-4.5.6?

Secondly, I did install Gromacs-5.0.4 for comparison, and I am using DSSP
2.0.4 again. This time I am using

do_dssp -f prot.xtc -s prot.tpr -ver 2

The output I am getting is shown below. Not sure what is going on.



















*There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp -i
ddJszHtZ -o ddRZ5pwg > /dev/null 2> /dev/null'Reading frame   0 time
0.000   Back Off! I just backed up ddJszHtZ to
./#ddJszHtZ.1#---Program
do_dssp, VERSION 5.0.4Source code file:
/home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
line: 670Fatal error:Failed to execute command: Try specifying your dssp
version with the -ver option.For more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
---*
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Re: [gmx-users] Regarding DSSP

[Justin Lemkul]

On 2/16/15 3:15 PM, HANNIBAL LECTER wrote:

Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is not
a scope to specify using the -ver command in this particular version as
opposed to the newer versions (5.0.4).

By '' I meant

do_dssp -f prot.xtc -s prot.tpr.

How do I specify a dssp version in gromacs-4.5.6?



I forget when the -ver flag was introduced.  Safe bet is if you're using an 
ancient GROMACS version, you need a similarly ancient DSSP (version 1.0.x).



Secondly, I did install Gromacs-5.0.4 for comparison, and I am using DSSP
2.0.4 again. This time I am using

do_dssp -f prot.xtc -s prot.tpr -ver 2

The output I am getting is shown below. Not sure what is going on.



















*There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp -i
ddJszHtZ -o ddRZ5pwg > /dev/null 2> /dev/null'Reading frame   0 time


My guess is that "mkdssp" is not actually the same thing as "dssp" - make sure 
you've installed a real, functional dssp binary.


-Justin


0.000   Back Off! I just backed up ddJszHtZ to
./#ddJszHtZ.1#---Program
do_dssp, VERSION 5.0.4Source code file:
/home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
line: 670Fatal error:Failed to execute command: Try specifying your dssp
version with the -ver option.For more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
---*



--
==

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] Regarding DSSP

[HANNIBAL LECTER]

Thanks for your reply. Couple of things.
I don't really know where to get older dssp binaries. I couldn't find them
available for download in the dssp website.

I renamed the mkdssp binary to dssp so I am sure nothing is wrong out there
when I export the binaries for utilization in gromacs.
On Feb 16, 2015 3:45 PM, "Justin Lemkul"  wrote:

>
>
> On 2/16/15 3:15 PM, HANNIBAL LECTER wrote:
>
>> Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is
>> not
>> a scope to specify using the -ver command in this particular version as
>> opposed to the newer versions (5.0.4).
>>
>> By '' I meant
>>
>> do_dssp -f prot.xtc -s prot.tpr.
>>
>> How do I specify a dssp version in gromacs-4.5.6?
>>
>>
> I forget when the -ver flag was introduced.  Safe bet is if you're using
> an ancient GROMACS version, you need a similarly ancient DSSP (version
> 1.0.x).
>
>  Secondly, I did install Gromacs-5.0.4 for comparison, and I am using DSSP
>> 2.0.4 again. This time I am using
>>
>> do_dssp -f prot.xtc -s prot.tpr -ver 2
>>
>> The output I am getting is shown below. Not sure what is going on.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp -i
>> ddJszHtZ -o ddRZ5pwg > /dev/null 2> /dev/null'Reading frame   0 time
>>
>
> My guess is that "mkdssp" is not actually the same thing as "dssp" - make
> sure you've installed a real, functional dssp binary.
>
> -Justin
>
>  0.000   Back Off! I just backed up ddJszHtZ to
>> ./#ddJszHtZ.1#--
>> -Program
>> do_dssp, VERSION 5.0.4Source code file:
>> /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
>> line: 670Fatal error:Failed to execute command: Try specifying your dssp
>> version with the -ver option.For more information and tips for
>> troubleshooting, please check the GROMACSwebsite at
>> http://www.gromacs.org/Documentation/Errors
>> -
>> --*
>>
>>
> --
> ==
>
> 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] Regarding DSSP

[Justin Lemkul]

On 2/16/15 4:07 PM, HANNIBAL LECTER wrote:

Thanks for your reply. Couple of things.
I don't really know where to get older dssp binaries. I couldn't find them
available for download in the dssp website.



http://swift.cmbi.ru.nl/gv/dssp/

Click on "Distributions" and at the bottom of that page, "DSSPold" is the old 
version.



I renamed the mkdssp binary to dssp so I am sure nothing is wrong out there
when I export the binaries for utilization in gromacs.


Aside from the usual advice of making sure the binary is actually executable 
(and actually runs, check with ./dssp -V for instance), there's little to go on 
here.


-Justin


On Feb 16, 2015 3:45 PM, "Justin Lemkul"  wrote:




On 2/16/15 3:15 PM, HANNIBAL LECTER wrote:


Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is
not
a scope to specify using the -ver command in this particular version as
opposed to the newer versions (5.0.4).

By '' I meant

do_dssp -f prot.xtc -s prot.tpr.

How do I specify a dssp version in gromacs-4.5.6?



I forget when the -ver flag was introduced.  Safe bet is if you're using
an ancient GROMACS version, you need a similarly ancient DSSP (version
1.0.x).

  Secondly, I did install Gromacs-5.0.4 for comparison, and I am using DSSP

2.0.4 again. This time I am using

do_dssp -f prot.xtc -s prot.tpr -ver 2

The output I am getting is shown below. Not sure what is going on.



















*There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp -i
ddJszHtZ -o ddRZ5pwg > /dev/null 2> /dev/null'Reading frame   0 time



My guess is that "mkdssp" is not actually the same thing as "dssp" - make
sure you've installed a real, functional dssp binary.

-Justin

  0.000   Back Off! I just backed up ddJszHtZ to

./#ddJszHtZ.1#--
-Program
do_dssp, VERSION 5.0.4Source code file:
/home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
line: 670Fatal error:Failed to execute command: Try specifying your dssp
version with the -ver option.For more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
-
--*



--
==

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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==

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] Problem in new version of Gromacs 5.0

[Faezeh Pousaneh]

Dear expert,

I have upgraded my Gromacs to latest version 5. I try to run my tested
simulations in new version, but strangely I see in VMD file of the
trajectory that some unwanted bonds occur during the simulation (I have
tried for difference molecules, even simple water). I wonder is there
something wrong in my .mdp file which must be adopted to the new version of
Gromacs, or is it some kind of effect of periodic boundaries condition
which appear in the VMD?

my .mdp file (which was working well in Gromacs4.6):


 integrator= md
 dt= 0.002
 nsteps= 100
 nstenergy = 1000; save energies every
 nstxtcout = 1   ; Output frequency for xtc file
 xtc-precision = 1   ; precision for xtc file
 ns_type   = grid; search neighboring grid cells
 nstlist   = 5   ;  fs
 pbc   = xyz ; 3-D PBC
 rlist = 1.0 ; short-range neighborlist cutoff
(in nm)
 rcoulomb  = 1.0 ; short-range electrostatic cutoff
(in nm)
 rvdw  = 1.0 ; short-range van der Waals cutoff
(in nm)
 coulombtype   = PME ; Particle Mesh Ewald for
long-range electrostatics
 pme_order = 4   ; cubic interpolation
 fourierspacing= 0.16; grid spacing for FFT
 vdw-type  = Cut-off
 Tcoupl= v-rescale   ; modified Berendsen thermostat
 tau_t = 0.1 ; time constant, in ps
 ref_t = 298.; reference temperature, one for
each group, in K
 tc-grps   = system
 Pcoupl= Parrinello-Rahman
 Pcoupltype= Isotropic
 tau_p = 1.0
 compressibility   = 4.5e-5
 ref_p = 1.0
 gen_vel   = no
 DispCorr  = EnerPres; account for cut-off vdW scheme
 constraints   = all-bonds   ; all bonds constrained (fixed
length)
 continuation  = yes ; Restarting after NPT
 constraint-algorithm  = lincs   ; holonomic constraints
 lincs_iter= 1   ; accuracy of LINCS
 lincs_order   = 4   ; also related to accuracy

many thanks in advance,

Best regards

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Re: [gmx-users] Problem in new version of Gromacs 5.0

[Justin Lemkul]

On 2/16/15 5:48 PM, Faezeh Pousaneh wrote:

Dear expert,

I have upgraded my Gromacs to latest version 5. I try to run my tested
simulations in new version, but strangely I see in VMD file of the
trajectory that some unwanted bonds occur during the simulation (I have
tried for difference molecules, even simple water). I wonder is there
something wrong in my .mdp file which must be adopted to the new version of
Gromacs, or is it some kind of effect of periodic boundaries condition
which appear in the VMD?



http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization

See #2.

-Justin


my .mdp file (which was working well in Gromacs4.6):


  integrator= md
  dt= 0.002
  nsteps= 100
  nstenergy = 1000; save energies every
  nstxtcout = 1   ; Output frequency for xtc file
  xtc-precision = 1   ; precision for xtc file
  ns_type   = grid; search neighboring grid cells
  nstlist   = 5   ;  fs
  pbc   = xyz ; 3-D PBC
  rlist = 1.0 ; short-range neighborlist cutoff
(in nm)
  rcoulomb  = 1.0 ; short-range electrostatic cutoff
(in nm)
  rvdw  = 1.0 ; short-range van der Waals cutoff
(in nm)
  coulombtype   = PME ; Particle Mesh Ewald for
long-range electrostatics
  pme_order = 4   ; cubic interpolation
  fourierspacing= 0.16; grid spacing for FFT
  vdw-type  = Cut-off
  Tcoupl= v-rescale   ; modified Berendsen thermostat
  tau_t = 0.1 ; time constant, in ps
  ref_t = 298.; reference temperature, one for
each group, in K
  tc-grps   = system
  Pcoupl= Parrinello-Rahman
  Pcoupltype= Isotropic
  tau_p = 1.0
  compressibility   = 4.5e-5
  ref_p = 1.0
  gen_vel   = no
  DispCorr  = EnerPres; account for cut-off vdW scheme
  constraints   = all-bonds   ; all bonds constrained (fixed
length)
  continuation  = yes ; Restarting after NPT
  constraint-algorithm  = lincs   ; holonomic constraints
  lincs_iter= 1   ; accuracy of LINCS
  lincs_order   = 4   ; also related to accuracy

many thanks in advance,

Best regards




--
==

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] Regarding DSSP

[HANNIBAL LECTER]

Okay, so the same errors seem to be persisting.

I am not sure what can possibly go wrong in this case. The dssp program
seems to be working (just typing dssp in the shell gives information
regarding the versions of dssp that has been used).

The dsspold program doesn't seem to be doing much.

Does anyone know of a version of DSSP executable corresponding to a working
Gromacs version?

On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul  wrote:

>
>
> On 2/16/15 4:07 PM, HANNIBAL LECTER wrote:
>
>> Thanks for your reply. Couple of things.
>> I don't really know where to get older dssp binaries. I couldn't find them
>> available for download in the dssp website.
>>
>>
> http://swift.cmbi.ru.nl/gv/dssp/
>
> Click on "Distributions" and at the bottom of that page, "DSSPold" is the
> old version.
>
>  I renamed the mkdssp binary to dssp so I am sure nothing is wrong out
>> there
>> when I export the binaries for utilization in gromacs.
>>
>
> Aside from the usual advice of making sure the binary is actually
> executable (and actually runs, check with ./dssp -V for instance), there's
> little to go on here.
>
> -Justin
>
>
>  On Feb 16, 2015 3:45 PM, "Justin Lemkul"  wrote:
>>
>>
>>>
>>> On 2/16/15 3:15 PM, HANNIBAL LECTER wrote:
>>>
>>>  Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is
 not
 a scope to specify using the -ver command in this particular version as
 opposed to the newer versions (5.0.4).

 By '' I meant

 do_dssp -f prot.xtc -s prot.tpr.

 How do I specify a dssp version in gromacs-4.5.6?


  I forget when the -ver flag was introduced.  Safe bet is if you're
>>> using
>>> an ancient GROMACS version, you need a similarly ancient DSSP (version
>>> 1.0.x).
>>>
>>>   Secondly, I did install Gromacs-5.0.4 for comparison, and I am using
>>> DSSP
>>>
 2.0.4 again. This time I am using

 do_dssp -f prot.xtc -s prot.tpr -ver 2

 The output I am getting is shown below. Not sure what is going on.



















 *There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp
 -i
 ddJszHtZ -o ddRZ5pwg > /dev/null 2> /dev/null'Reading frame   0 time


>>> My guess is that "mkdssp" is not actually the same thing as "dssp" - make
>>> sure you've installed a real, functional dssp binary.
>>>
>>> -Justin
>>>
>>>   0.000   Back Off! I just backed up ddJszHtZ to
>>>
 ./#ddJszHtZ.1#--
 -Program
 do_dssp, VERSION 5.0.4Source code file:
 /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
 line: 670Fatal error:Failed to execute command: Try specifying your dssp
 version with the -ver option.For more information and tips for
 troubleshooting, please check the GROMACSwebsite at
 http://www.gromacs.org/Documentation/Errors
 -
 --*


  --
>>> ==
>>>
>>> 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
>>>
>>> ==
>>> --
>>> 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.
>>>
>>>
> --
> ==
>
> 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
>
> ==
> --
> 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.
>
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Re: [gmx-users] Regarding DSSP

[Justin Lemkul]

On 2/16/15 6:20 PM, HANNIBAL LECTER wrote:

Okay, so the same errors seem to be persisting.

I am not sure what can possibly go wrong in this case. The dssp program
seems to be working (just typing dssp in the shell gives information
regarding the versions of dssp that has been used).

The dsspold program doesn't seem to be doing much.



No idea what that means, so I can't help with that.


Does anyone know of a version of DSSP executable corresponding to a working
Gromacs version?



DSSP 2.0.4 works with GROMACS 5.0.4 for sure (I ran it just the other day), but 
in principle any 2.x version should work with GROMACS 4.6 or newer (the issue 
was closed 3 years ago, with minimal reported issues and no code modifications 
since).


-Justin


On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul  wrote:




On 2/16/15 4:07 PM, HANNIBAL LECTER wrote:


Thanks for your reply. Couple of things.
I don't really know where to get older dssp binaries. I couldn't find them
available for download in the dssp website.



http://swift.cmbi.ru.nl/gv/dssp/

Click on "Distributions" and at the bottom of that page, "DSSPold" is the
old version.

  I renamed the mkdssp binary to dssp so I am sure nothing is wrong out

there
when I export the binaries for utilization in gromacs.



Aside from the usual advice of making sure the binary is actually
executable (and actually runs, check with ./dssp -V for instance), there's
little to go on here.

-Justin


  On Feb 16, 2015 3:45 PM, "Justin Lemkul"  wrote:





On 2/16/15 3:15 PM, HANNIBAL LECTER wrote:

  Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is

not
a scope to specify using the -ver command in this particular version as
opposed to the newer versions (5.0.4).

By '' I meant

do_dssp -f prot.xtc -s prot.tpr.

How do I specify a dssp version in gromacs-4.5.6?


  I forget when the -ver flag was introduced.  Safe bet is if you're

using
an ancient GROMACS version, you need a similarly ancient DSSP (version
1.0.x).

   Secondly, I did install Gromacs-5.0.4 for comparison, and I am using
DSSP


2.0.4 again. This time I am using

do_dssp -f prot.xtc -s prot.tpr -ver 2

The output I am getting is shown below. Not sure what is going on.



















*There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp
-i
ddJszHtZ -o ddRZ5pwg > /dev/null 2> /dev/null'Reading frame   0 time



My guess is that "mkdssp" is not actually the same thing as "dssp" - make
sure you've installed a real, functional dssp binary.

-Justin

   0.000   Back Off! I just backed up ddJszHtZ to


./#ddJszHtZ.1#--
-Program
do_dssp, VERSION 5.0.4Source code file:
/home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
line: 670Fatal error:Failed to execute command: Try specifying your dssp
version with the -ver option.For more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
-
--*


  --

==

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

==
--
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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* 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.



--
==

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

==
--
Gromacs Users mailing list

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Support/Mailing_Lists/GMX-Users_List before posting!

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* For (un)subscribe requests visit
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send a mail to gmx-users-requ...@gromacs.org.



--
==

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...@outerban

Re: [gmx-users] Regarding DSSP

[HANNIBAL LECTER]

Okay. what can be possibly wrong? I mean if someone CAN run Gromacs-5.0.4 +
DSSP 2.0.4, it should be running in other systems as well unless I am
messing something up. So I list my steps.

1. Download the executable from
ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/ (not the source code, but
just the binaries).

2. rename the file to dssp204
3. chmod +x dssp204
4. sudo mv dssp204 /usr/local/bin/
5. export DSSP=/usr/loca/bin/dssp204
6. do_dssp -f data/xtc/traj.xtc -s data/tpr/topol.tpr -ver 2

What can be possibly wrong?


The output is shown below:








































*Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single
precision)Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6
(single precision)Group 0 ( System) has 10901 elementsGroup
1 (Protein) has   121 elementsGroup 2 (  Protein-H) has
68 elementsGroup 3 (C-alpha) has16 elementsGroup 4
(   Backbone) has50 elementsGroup 5 (  MainChain) has67
elementsGroup 6 (   MainChain+Cb) has67 elementsGroup 7 (
MainChain+H) has85 elementsGroup 8 (  SideChain) has36
elementsGroup 9 (SideChain-H) has 1 elementsGroup10 (
Prot-Masses) has   121 elementsGroup11 (non-Protein) has 10780
elementsGroup12 (  Other) has  2320 elementsGroup13
(RS1) has  2320 elementsGroup14 (  Water) has  8460
elementsGroup15 (SOL) has  8460 elementsGroup16 (
non-Water) has  2441 elementsSelect a group: 1Selected 1: 'Protein'There
are 18 residues in your selected groupdssp cmd='/usr/bin/dssp20464 -i
ddUkWy9e -o dd7htL6i > /dev/null 2> /dev/null'Reading frame   0 time
0.000   Back Off! I just backed up ddUkWy9e to
./#ddUkWy9e.1#---Program
gmx, VERSION 5.0.4Source code file:
/home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
line: 670Fatal error:Failed to execute command: Try specifying your dssp
version with the -ver option.For more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
---*


On Mon, Feb 16, 2015 at 6:25 PM, Justin Lemkul  wrote:

>
>
> On 2/16/15 6:20 PM, HANNIBAL LECTER wrote:
>
>> Okay, so the same errors seem to be persisting.
>>
>> I am not sure what can possibly go wrong in this case. The dssp program
>> seems to be working (just typing dssp in the shell gives information
>> regarding the versions of dssp that has been used).
>>
>> The dsspold program doesn't seem to be doing much.
>>
>>
> No idea what that means, so I can't help with that.
>
>  Does anyone know of a version of DSSP executable corresponding to a
>> working
>> Gromacs version?
>>
>>
> DSSP 2.0.4 works with GROMACS 5.0.4 for sure (I ran it just the other
> day), but in principle any 2.x version should work with GROMACS 4.6 or
> newer (the issue was closed 3 years ago, with minimal reported issues and
> no code modifications since).
>
> -Justin
>
>
>  On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 2/16/15 4:07 PM, HANNIBAL LECTER wrote:
>>>
>>>  Thanks for your reply. Couple of things.
 I don't really know where to get older dssp binaries. I couldn't find
 them
 available for download in the dssp website.


  http://swift.cmbi.ru.nl/gv/dssp/
>>>
>>> Click on "Distributions" and at the bottom of that page, "DSSPold" is the
>>> old version.
>>>
>>>   I renamed the mkdssp binary to dssp so I am sure nothing is wrong out
>>>
 there
 when I export the binaries for utilization in gromacs.


>>> Aside from the usual advice of making sure the binary is actually
>>> executable (and actually runs, check with ./dssp -V for instance),
>>> there's
>>> little to go on here.
>>>
>>> -Justin
>>>
>>>
>>>   On Feb 16, 2015 3:45 PM, "Justin Lemkul"  wrote:
>>>



> On 2/16/15 3:15 PM, HANNIBAL LECTER wrote:
>
>   Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there
> is
>
>> not
>> a scope to specify using the -ver command in this particular version
>> as
>> opposed to the newer versions (5.0.4).
>>
>> By '' I meant
>>
>> do_dssp -f prot.xtc -s prot.tpr.
>>
>> How do I specify a dssp version in gromacs-4.5.6?
>>
>>
>>   I forget when the -ver flag was introduced.  Safe bet is if you're
>>
> using
> an ancient GROMACS version, you need a similarly ancient DSSP (version
> 1.0.x).
>
>Secondly, I did install Gromacs-5.0.4 for comparison, and I am using
> DSSP
>
>  2.0.4 again. This time I am using
>>
>> do_dssp -f prot.xtc -s prot.tpr -ver 2
>>
>> The output I am getting is shown below. Not sure what is going on.
>>
>>
>>
>>
>>

Re: [gmx-users] Regarding DSSP

[Justin Lemkul]

On 2/16/15 6:40 PM, HANNIBAL LECTER wrote:

Okay. what can be possibly wrong? I mean if someone CAN run Gromacs-5.0.4 +
DSSP 2.0.4, it should be running in other systems as well unless I am
messing something up. So I list my steps.

1. Download the executable from
ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/ (not the source code, but
just the binaries).

2. rename the file to dssp204
3. chmod +x dssp204
4. sudo mv dssp204 /usr/local/bin/
5. export DSSP=/usr/loca/bin/dssp204
6. do_dssp -f data/xtc/traj.xtc -s data/tpr/topol.tpr -ver 2

What can be possibly wrong?



Not sure, because what you're telling us isn't consistent:

1. You're not copying and pasting (or you are and you're setting variables 
wrong) because step 4 shows "/usr/loca/bin" as the location of the executable, 
which in step 3 you (presumably) put in /usr/local/bin (which actually makes sense).


2. That's not what you did because:

dssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i > /dev/null 2> /dev/null'

says you have installed something called "dssp20464" in /usr/bin.

It's hard to troubleshoot something when you're not giving us consistent 
information.  If the suffix "20464" indicates version "2.0.4" and 64-bit 
architecture, is that appropriate for your system?  You have a 64-bit system, 
not 32-bit?


-Justin



The output is shown below:








































*Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single
precision)Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6
(single precision)Group 0 ( System) has 10901 elementsGroup
1 (Protein) has   121 elementsGroup 2 (  Protein-H) has
68 elementsGroup 3 (C-alpha) has16 elementsGroup 4
(   Backbone) has50 elementsGroup 5 (  MainChain) has67
elementsGroup 6 (   MainChain+Cb) has67 elementsGroup 7 (
MainChain+H) has85 elementsGroup 8 (  SideChain) has36
elementsGroup 9 (SideChain-H) has 1 elementsGroup10 (
Prot-Masses) has   121 elementsGroup11 (non-Protein) has 10780
elementsGroup12 (  Other) has  2320 elementsGroup13
(RS1) has  2320 elementsGroup14 (  Water) has  8460
elementsGroup15 (SOL) has  8460 elementsGroup16 (
non-Water) has  2441 elementsSelect a group: 1Selected 1: 'Protein'There
are 18 residues in your selected groupdssp cmd='/usr/bin/dssp20464 -i
ddUkWy9e -o dd7htL6i > /dev/null 2> /dev/null'Reading frame   0 time
0.000   Back Off! I just backed up ddUkWy9e to
./#ddUkWy9e.1#---Program
gmx, VERSION 5.0.4Source code file:
/home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
line: 670Fatal error:Failed to execute command: Try specifying your dssp
version with the -ver option.For more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
---*


On Mon, Feb 16, 2015 at 6:25 PM, Justin Lemkul  wrote:




On 2/16/15 6:20 PM, HANNIBAL LECTER wrote:


Okay, so the same errors seem to be persisting.

I am not sure what can possibly go wrong in this case. The dssp program
seems to be working (just typing dssp in the shell gives information
regarding the versions of dssp that has been used).

The dsspold program doesn't seem to be doing much.



No idea what that means, so I can't help with that.

  Does anyone know of a version of DSSP executable corresponding to a

working
Gromacs version?



DSSP 2.0.4 works with GROMACS 5.0.4 for sure (I ran it just the other
day), but in principle any 2.x version should work with GROMACS 4.6 or
newer (the issue was closed 3 years ago, with minimal reported issues and
no code modifications since).

-Justin


  On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul  wrote:





On 2/16/15 4:07 PM, HANNIBAL LECTER wrote:

  Thanks for your reply. Couple of things.

I don't really know where to get older dssp binaries. I couldn't find
them
available for download in the dssp website.


  http://swift.cmbi.ru.nl/gv/dssp/


Click on "Distributions" and at the bottom of that page, "DSSPold" is the
old version.

   I renamed the mkdssp binary to dssp so I am sure nothing is wrong out


there
when I export the binaries for utilization in gromacs.



Aside from the usual advice of making sure the binary is actually
executable (and actually runs, check with ./dssp -V for instance),
there's
little to go on here.

-Justin


   On Feb 16, 2015 3:45 PM, "Justin Lemkul"  wrote:






On 2/16/15 3:15 PM, HANNIBAL LECTER wrote:

   Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there
is


not
a scope to specify using the -ver command in this particular version
as
opposed to the newer versions (5.0.4).

By '' I meant

do_dssp -f prot.xtc -s prot.tpr.

How do I specify a dssp version in grom

Re: [gmx-users] Regarding DSSP

[HANNIBAL LECTER]

Sorry, yes, I actually made a copy and pasted in the /usr/bin directory as
well. So there IS actually a copy of the same program.

Yes, my system is 64 bit. Just as a test case, I tried with the 32-bit
version as well. Same error as above.

On Mon, Feb 16, 2015 at 6:45 PM, Justin Lemkul  wrote:

>
>
> On 2/16/15 6:40 PM, HANNIBAL LECTER wrote:
>
>> Okay. what can be possibly wrong? I mean if someone CAN run Gromacs-5.0.4
>> +
>> DSSP 2.0.4, it should be running in other systems as well unless I am
>> messing something up. So I list my steps.
>>
>> 1. Download the executable from
>> ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/ (not the source code,
>> but
>> just the binaries).
>>
>> 2. rename the file to dssp204
>> 3. chmod +x dssp204
>> 4. sudo mv dssp204 /usr/local/bin/
>> 5. export DSSP=/usr/loca/bin/dssp204
>> 6. do_dssp -f data/xtc/traj.xtc -s data/tpr/topol.tpr -ver 2
>>
>> What can be possibly wrong?
>>
>>
> Not sure, because what you're telling us isn't consistent:
>
> 1. You're not copying and pasting (or you are and you're setting variables
> wrong) because step 4 shows "/usr/loca/bin" as the location of the
> executable, which in step 3 you (presumably) put in /usr/local/bin (which
> actually makes sense).
>
> 2. That's not what you did because:
>
> dssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i > /dev/null 2>
> /dev/null'
>
> says you have installed something called "dssp20464" in /usr/bin.
>
> It's hard to troubleshoot something when you're not giving us consistent
> information.  If the suffix "20464" indicates version "2.0.4" and 64-bit
> architecture, is that appropriate for your system?  You have a 64-bit
> system, not 32-bit?
>
> -Justin
>
>
>> The output is shown below:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single
>> precision)Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6
>> (single precision)Group 0 ( System) has 10901 elementsGroup
>> 1 (Protein) has   121 elementsGroup 2 (  Protein-H) has
>> 68 elementsGroup 3 (C-alpha) has16 elementsGroup 4
>> (   Backbone) has50 elementsGroup 5 (  MainChain) has
>> 67
>> elementsGroup 6 (   MainChain+Cb) has67 elementsGroup 7 (
>> MainChain+H) has85 elementsGroup 8 (  SideChain) has36
>> elementsGroup 9 (SideChain-H) has 1 elementsGroup10 (
>> Prot-Masses) has   121 elementsGroup11 (non-Protein) has 10780
>> elementsGroup12 (  Other) has  2320 elementsGroup13
>> (RS1) has  2320 elementsGroup14 (  Water) has
>> 8460
>> elementsGroup15 (SOL) has  8460 elementsGroup16 (
>> non-Water) has  2441 elementsSelect a group: 1Selected 1: 'Protein'There
>> are 18 residues in your selected groupdssp cmd='/usr/bin/dssp20464 -i
>> ddUkWy9e -o dd7htL6i > /dev/null 2> /dev/null'Reading frame   0 time
>> 0.000   Back Off! I just backed up ddUkWy9e to
>> ./#ddUkWy9e.1#--
>> -Program
>> gmx, VERSION 5.0.4Source code file:
>>
>> /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
>> line: 670Fatal error:Failed to execute command: Try specifying your dssp
>> version with the -ver option.For more information and tips for
>> troubleshooting, please check the GROMACSwebsite at
>> http://www.gromacs.org/Documentation/Errors
>> -
>> --*
>>
>>
>> On Mon, Feb 16, 2015 at 6:25 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 2/16/15 6:20 PM, HANNIBAL LECTER wrote:
>>>
>>>  Okay, so the same errors seem to be persisting.

 I am not sure what can possibly go wrong in this case. The dssp program
 seems to be working (just typing dssp in the shell gives information
 regarding the versions of dssp that has been used).

 The dsspold program doesn't seem to be doing much.


  No idea what that means, so I can't help with that.
>>>
>>>   Does anyone know of a version of DSSP executable corresponding to a
>>>
 working
 Gromacs version?


  DSSP 2.0.4 works with GROMACS 5.0.4 for sure (I ran it just the other
>>> day), but in principle any 2.x version should work with GROMACS 4.6 or
>>> newer (the issue was closed 3 years ago, with minimal reported issues and
>>> no code modifications since).
>>>
>>> -Justin
>>>
>>>
>>>   On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul 
>>> wrote:
>>>



> On 2/16/15 4:07 PM, HANNIBAL LECTER wrote:
>
>   Thanks for your reply. Couple of things.
>
>> I don't really know where to get older dssp binaries. I couldn't find
>> them
>> available for download in the dssp website.
>>
>>
>>   http://swift.cmbi.ru.nl/gv/dssp/
>>
>
> Click on "Dis

Re: [gmx-users] Regarding DSSP

[Justin Lemkul]

On 2/16/15 6:55 PM, HANNIBAL LECTER wrote:

Sorry, yes, I actually made a copy and pasted in the /usr/bin directory as
well. So there IS actually a copy of the same program.

Yes, my system is 64 bit. Just as a test case, I tried with the 32-bit
version as well. Same error as above.



Does the dssp binary work when you run it on a single .pdb file (as it's 
designed to do)?  If not, then the binary is (somehow) incompatible with your 
machine.  Compiling from source would fix that.


-Justin


On Mon, Feb 16, 2015 at 6:45 PM, Justin Lemkul  wrote:




On 2/16/15 6:40 PM, HANNIBAL LECTER wrote:


Okay. what can be possibly wrong? I mean if someone CAN run Gromacs-5.0.4
+
DSSP 2.0.4, it should be running in other systems as well unless I am
messing something up. So I list my steps.

1. Download the executable from
ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/ (not the source code,
but
just the binaries).

2. rename the file to dssp204
3. chmod +x dssp204
4. sudo mv dssp204 /usr/local/bin/
5. export DSSP=/usr/loca/bin/dssp204
6. do_dssp -f data/xtc/traj.xtc -s data/tpr/topol.tpr -ver 2

What can be possibly wrong?



Not sure, because what you're telling us isn't consistent:

1. You're not copying and pasting (or you are and you're setting variables
wrong) because step 4 shows "/usr/loca/bin" as the location of the
executable, which in step 3 you (presumably) put in /usr/local/bin (which
actually makes sense).

2. That's not what you did because:

dssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i > /dev/null 2>
/dev/null'

says you have installed something called "dssp20464" in /usr/bin.

It's hard to troubleshoot something when you're not giving us consistent
information.  If the suffix "20464" indicates version "2.0.4" and 64-bit
architecture, is that appropriate for your system?  You have a 64-bit
system, not 32-bit?

-Justin



The output is shown below:








































*Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single
precision)Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6
(single precision)Group 0 ( System) has 10901 elementsGroup
1 (Protein) has   121 elementsGroup 2 (  Protein-H) has
68 elementsGroup 3 (C-alpha) has16 elementsGroup 4
(   Backbone) has50 elementsGroup 5 (  MainChain) has
67
elementsGroup 6 (   MainChain+Cb) has67 elementsGroup 7 (
MainChain+H) has85 elementsGroup 8 (  SideChain) has36
elementsGroup 9 (SideChain-H) has 1 elementsGroup10 (
Prot-Masses) has   121 elementsGroup11 (non-Protein) has 10780
elementsGroup12 (  Other) has  2320 elementsGroup13
(RS1) has  2320 elementsGroup14 (  Water) has
8460
elementsGroup15 (SOL) has  8460 elementsGroup16 (
non-Water) has  2441 elementsSelect a group: 1Selected 1: 'Protein'There
are 18 residues in your selected groupdssp cmd='/usr/bin/dssp20464 -i
ddUkWy9e -o dd7htL6i > /dev/null 2> /dev/null'Reading frame   0 time
0.000   Back Off! I just backed up ddUkWy9e to
./#ddUkWy9e.1#--
-Program
gmx, VERSION 5.0.4Source code file:

/home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
line: 670Fatal error:Failed to execute command: Try specifying your dssp
version with the -ver option.For more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
-
--*


On Mon, Feb 16, 2015 at 6:25 PM, Justin Lemkul  wrote:




On 2/16/15 6:20 PM, HANNIBAL LECTER wrote:

  Okay, so the same errors seem to be persisting.


I am not sure what can possibly go wrong in this case. The dssp program
seems to be working (just typing dssp in the shell gives information
regarding the versions of dssp that has been used).

The dsspold program doesn't seem to be doing much.


  No idea what that means, so I can't help with that.


   Does anyone know of a version of DSSP executable corresponding to a


working
Gromacs version?


  DSSP 2.0.4 works with GROMACS 5.0.4 for sure (I ran it just the other

day), but in principle any 2.x version should work with GROMACS 4.6 or
newer (the issue was closed 3 years ago, with minimal reported issues and
no code modifications since).

-Justin


   On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul 
wrote:






On 2/16/15 4:07 PM, HANNIBAL LECTER wrote:

   Thanks for your reply. Couple of things.


I don't really know where to get older dssp binaries. I couldn't find
them
available for download in the dssp website.


   http://swift.cmbi.ru.nl/gv/dssp/



Click on "Distributions" and at the bottom of that page, "DSSPold" is
the
old version.

I renamed the mkdssp binary to dssp so I am sure nothing is wrong
out

  there

when I export the binaries for utilization in grom

Re: [gmx-users] Regarding DSSP

[HANNIBAL LECTER]

Yes, the binary is working on a single pdb file.

On Mon, Feb 16, 2015 at 7:06 PM, Justin Lemkul  wrote:

>
>
> On 2/16/15 6:55 PM, HANNIBAL LECTER wrote:
>
>> Sorry, yes, I actually made a copy and pasted in the /usr/bin directory as
>> well. So there IS actually a copy of the same program.
>>
>> Yes, my system is 64 bit. Just as a test case, I tried with the 32-bit
>> version as well. Same error as above.
>>
>>
> Does the dssp binary work when you run it on a single .pdb file (as it's
> designed to do)?  If not, then the binary is (somehow) incompatible with
> your machine.  Compiling from source would fix that.
>
> -Justin
>
>  On Mon, Feb 16, 2015 at 6:45 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 2/16/15 6:40 PM, HANNIBAL LECTER wrote:
>>>
>>>  Okay. what can be possibly wrong? I mean if someone CAN run
 Gromacs-5.0.4
 +
 DSSP 2.0.4, it should be running in other systems as well unless I am
 messing something up. So I list my steps.

 1. Download the executable from
 ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/ (not the source code,
 but
 just the binaries).

 2. rename the file to dssp204
 3. chmod +x dssp204
 4. sudo mv dssp204 /usr/local/bin/
 5. export DSSP=/usr/loca/bin/dssp204
 6. do_dssp -f data/xtc/traj.xtc -s data/tpr/topol.tpr -ver 2

 What can be possibly wrong?


  Not sure, because what you're telling us isn't consistent:
>>>
>>> 1. You're not copying and pasting (or you are and you're setting
>>> variables
>>> wrong) because step 4 shows "/usr/loca/bin" as the location of the
>>> executable, which in step 3 you (presumably) put in /usr/local/bin (which
>>> actually makes sense).
>>>
>>> 2. That's not what you did because:
>>>
>>> dssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i > /dev/null 2>
>>> /dev/null'
>>>
>>> says you have installed something called "dssp20464" in /usr/bin.
>>>
>>> It's hard to troubleshoot something when you're not giving us consistent
>>> information.  If the suffix "20464" indicates version "2.0.4" and 64-bit
>>> architecture, is that appropriate for your system?  You have a 64-bit
>>> system, not 32-bit?
>>>
>>> -Justin
>>>
>>>
>>>  The output is shown below:








































 *Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single
 precision)Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6
 (single precision)Group 0 ( System) has 10901 elementsGroup
 1 (Protein) has   121 elementsGroup 2 (  Protein-H) has
 68 elementsGroup 3 (C-alpha) has16 elementsGroup 4
 (   Backbone) has50 elementsGroup 5 (  MainChain) has
 67
 elementsGroup 6 (   MainChain+Cb) has67 elementsGroup 7 (
 MainChain+H) has85 elementsGroup 8 (  SideChain) has36
 elementsGroup 9 (SideChain-H) has 1 elementsGroup10 (
 Prot-Masses) has   121 elementsGroup11 (non-Protein) has 10780
 elementsGroup12 (  Other) has  2320 elementsGroup13
 (RS1) has  2320 elementsGroup14 (  Water) has
 8460
 elementsGroup15 (SOL) has  8460 elementsGroup16 (
 non-Water) has  2441 elementsSelect a group: 1Selected 1: 'Protein'There
 are 18 residues in your selected groupdssp cmd='/usr/bin/dssp20464 -i
 ddUkWy9e -o dd7htL6i > /dev/null 2> /dev/null'Reading frame   0 time
 0.000   Back Off! I just backed up ddUkWy9e to
 ./#ddUkWy9e.1#--
 -Program
 gmx, VERSION 5.0.4Source code file:

 /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
 line: 670Fatal error:Failed to execute command: Try specifying your dssp
 version with the -ver option.For more information and tips for
 troubleshooting, please check the GROMACSwebsite at
 http://www.gromacs.org/Documentation/Errors
 -
 --*


 On Mon, Feb 16, 2015 at 6:25 PM, Justin Lemkul  wrote:



> On 2/16/15 6:20 PM, HANNIBAL LECTER wrote:
>
>   Okay, so the same errors seem to be persisting.
>
>>
>> I am not sure what can possibly go wrong in this case. The dssp
>> program
>> seems to be working (just typing dssp in the shell gives information
>> regarding the versions of dssp that has been used).
>>
>> The dsspold program doesn't seem to be doing much.
>>
>>
>>   No idea what that means, so I can't help with that.
>>
>
>Does anyone know of a version of DSSP executable corresponding to a
>
>  working
>> Gromacs version?
>>
>>

Re: [gmx-users] Semiisotropic pressure coupling

[shivangi nangia]

Hello Justin,

I have a follow up question.

The non-bonded parameters you have pointed out to :
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

is valid if the system contains only lipid or it should be use with a
system containing lipid and protein too.

Thanks,

sxn


On Mon, Feb 16, 2015 at 2:10 PM, shivangi nangia 
wrote:

> Thanks a lot Justin!!!
>
>
>
>
>
>
> On Sun, Feb 15, 2015 at 1:13 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 2/15/15 1:02 PM, shivangi nangia wrote:
>>
>>> Dear Justin,
>>>
>>> Thanks for the continuous help.
>>>
>>> Since I have done reverse CG, The CG POPC was equilibrated alone
>>> anisotropically, The APL was fine there.
>>> On reverse CG and NVT its still fine, it only after NPT it starts
>>> dropping.
>>>
>>>
>> Of course it's fine during NVT - the box can't change so the area is
>> constant.
>>
>>  I am calculating APL as (2*Lx*Ly)/(No. of Lipids).
>>>
>>>
>> That's only valid for pure, symmetric membranes.  You have a protein
>> embedded in one leaflet, so this method is wrong.
>>
>>  You mentioned to get gull force field from your site, is it here:
>>>
>>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>>>
>>>
>> Yes, that's the right place.
>>
>>  On unzipping this I see POPC is an .trp entry.
>>>
>>> If there is some other database, kindly point it out to me.
>>>
>>>
>> What I'm telling you is to use those force field files to (1) verify that
>> your POPC parameters are right (they should be) and (2) you'll have the
>> right protein topology (there are different bonded parameters that will
>> affect protein dynamics).
>>
>> Again, I must emphasize - troubleshooting the APL of this system with
>> respect to the known APL of pure POPC is pointless.  You have a protein
>> that convolutes (and potentially changes) everything.  If you want to
>> simulate pure POPC to verify that things are fine, do that.  But taking
>> more time on any perceived discrepancies here is not productive.
>>
>>
>> -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] Double counting of h-bonds g_hbond:issue

[Udaya Dahal]

Hi All,

When I used the g_hbond the hydrogen bonding i was getting was quite good
but when I checked the index file i find double counting of the bonds. So
far, it seems to me that g_hbond is giving higher than the real hydrogen
bonds present in the system. For eg. in the following OW-HW-oxygen, we see
there are two bonds between 109(OW) and 110(HW) for two different polymer
oxygens.

Can anyone explain this issue?

 76 77 12
100101 47
109110 40--->1 (same hydrogen with two different oxygens)
109110 54--->2(same hydrogen with two different oxygens)
211212 54
211212 68
337338 68
343344  5
343344 19
403404 61
487488  5
511512 26
511512 40
538539 33
592593 12
592593 26

Hbnum.xvg shows
hydrogen bonds pairs within 0.35
16   8


Regards,
Udaya
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Re: [gmx-users] Problem executing do_dssp in gromacs

[Aarti rana]

After issuing command as you asked:

>echo $DSSP
>/usr/local/bin/dssp

And yes I downloaded the "dssp-2.0.4-linux-amd64
" file from
dssp site.


On Mon, Feb 16, 2015 at 11:52 PM, Justin Lemkul  wrote:

>
>
> After looking at this a bit more closely for someone else who asked the
> same question, your clue is here:
>
> dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a > /dev/null 2>
> /dev/null'
>
> For some reason your do_dssp command is triggering version 1 syntax.  A
> version 2 command should be something like:
>
> dssp cmd='/usr/local/bin/dssp -i ddYB5REk -o ddxi1TAx > /dev/null 2>
> /dev/null'
>
> Note the difference in -i/-o vs. -na.  This is the nature of the problem
> when dealing with different versions.  Somehow there's a disconnect between
> your DSSP version or the command you're telling us you're issuing.
>
>
> -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
>
> ==
> --
> 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.
>



-- 
*Happy and Healthy mantra  of life :  Enjoy what you have now, stop
collecting luxuries of life, because an unsatisfied person cannot relish
the precious moments of life, stay happy, stay cool, keep smiling, stay
away from arguments and controversies.*
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Re: [gmx-users] Regarding DSSP

[Mark Abraham]

Hi,

Exactly what dssp command worked? Your use of do_dssp must be consistent
with that. You must be making a specific error, so general descriptions of
your actions are likely to be counterproductive. :-) Please don't filter
things through your head, because that assumes you are doing the right
things, and the evidence is against that! :-)

Mark

On Feb 17, 2015 1:14 AM, "HANNIBAL LECTER" 
wrote:
>
> Yes, the binary is working on a single pdb file.
>
> On Mon, Feb 16, 2015 at 7:06 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 2/16/15 6:55 PM, HANNIBAL LECTER wrote:
> >
> >> Sorry, yes, I actually made a copy and pasted in the /usr/bin
directory as
> >> well. So there IS actually a copy of the same program.
> >>
> >> Yes, my system is 64 bit. Just as a test case, I tried with the 32-bit
> >> version as well. Same error as above.
> >>
> >>
> > Does the dssp binary work when you run it on a single .pdb file (as it's
> > designed to do)?  If not, then the binary is (somehow) incompatible with
> > your machine.  Compiling from source would fix that.
> >
> > -Justin
> >
> >  On Mon, Feb 16, 2015 at 6:45 PM, Justin Lemkul  wrote:
> >>
> >>
> >>>
> >>> On 2/16/15 6:40 PM, HANNIBAL LECTER wrote:
> >>>
> >>>  Okay. what can be possibly wrong? I mean if someone CAN run
>  Gromacs-5.0.4
>  +
>  DSSP 2.0.4, it should be running in other systems as well unless I am
>  messing something up. So I list my steps.
> 
>  1. Download the executable from
>  ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/ (not the source
code,
>  but
>  just the binaries).
> 
>  2. rename the file to dssp204
>  3. chmod +x dssp204
>  4. sudo mv dssp204 /usr/local/bin/
>  5. export DSSP=/usr/loca/bin/dssp204
>  6. do_dssp -f data/xtc/traj.xtc -s data/tpr/topol.tpr -ver 2
> 
>  What can be possibly wrong?
> 
> 
>   Not sure, because what you're telling us isn't consistent:
> >>>
> >>> 1. You're not copying and pasting (or you are and you're setting
> >>> variables
> >>> wrong) because step 4 shows "/usr/loca/bin" as the location of the
> >>> executable, which in step 3 you (presumably) put in /usr/local/bin
(which
> >>> actually makes sense).
> >>>
> >>> 2. That's not what you did because:
> >>>
> >>> dssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i > /dev/null 2>
> >>> /dev/null'
> >>>
> >>> says you have installed something called "dssp20464" in /usr/bin.
> >>>
> >>> It's hard to troubleshoot something when you're not giving us
consistent
> >>> information.  If the suffix "20464" indicates version "2.0.4" and
64-bit
> >>> architecture, is that appropriate for your system?  You have a 64-bit
> >>> system, not 32-bit?
> >>>
> >>> -Justin
> >>>
> >>>
> >>>  The output is shown below:
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>  *Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single
>  precision)Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6
>  (single precision)Group 0 ( System) has 10901
elementsGroup
>  1 (Protein) has   121 elementsGroup 2 (  Protein-H)
has
>  68 elementsGroup 3 (C-alpha) has16 elementsGroup
 4
>  (   Backbone) has50 elementsGroup 5 (  MainChain) has
>  67
>  elementsGroup 6 (   MainChain+Cb) has67 elementsGroup 7 (
>  MainChain+H) has85 elementsGroup 8 (  SideChain) has
36
>  elementsGroup 9 (SideChain-H) has 1 elementsGroup10 (
>  Prot-Masses) has   121 elementsGroup11 (non-Protein) has
10780
>  elementsGroup12 (  Other) has  2320 elementsGroup13
>  (RS1) has  2320 elementsGroup14 (  Water) has
>  8460
>  elementsGroup15 (SOL) has  8460 elementsGroup16 (
>  non-Water) has  2441 elementsSelect a group: 1Selected 1:
'Protein'There
>  are 18 residues in your selected groupdssp cmd='/usr/bin/dssp20464 -i
>  ddUkWy9e -o dd7htL6i > /dev/null 2> /dev/null'Reading frame   0
time
>  0.000   Back Off! I just backed up ddUkWy9e to
>  ./#ddUkWy9e.1#--
>  -Program
>  gmx, VERSION 5.0.4Source code file:
> 
> 
/home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
>  line: 670Fatal error:Failed to execute command: Try specifying your
dssp
>  version with the -ver option.For more information and tips for
>  troubleshooting, please check the GROMACSwebsite at
>  http://www.gromacs.org/Documentation/Errors
>  -
>  --*
> 
> 
>  On Mon, Feb 16, 

Re: [gmx-users] lower Area per lipid for DPPC with CHARMM36

[tarak karmakar]

Hi Justin,
Still there is some problem. In the short equilibration I've got the good
value of the Area per lipid. But now in the production run, it kept on
decreasing. Presently, the value is ~56 A^2. The following .mdp has been
used.

--
title= NPT
integrator= md; Algorithm ("md" = molecular dynamics [leap-frog
integrator]; "md-vv" = md using velocity verlet; sd = stochastic dynamics)
dt= 0.002; Time-step (ps)
nsteps= 500; Number of steps to run (0.002 * 50 = 1 ns)

; Parameters controlling output writing
nstxout= 1 ; Write coordinates to output .trr file
every 2 ps
nstvout= 1 ; Write velocities to output .trr file every
2 ps
nstenergy= 1 ; Write energies to output .edr file every 2 ps
nstlog= 1000 ; Write output to .log file every 2 ps

; 7.3.9 Neighbor Searching
nstlist = 10; [steps] freq to update neighbor
list
ns_type = grid  ; method of updating neighbor list
pbc = xyz   ; periodic boundary conditions in
all directions

cutoff-scheme = Verlet

vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0


; 7.3.10 Electrostatics
coulombtype = PME   ; Particle-Mesh Ewald electrostatics
rcoulomb= 1.2   ; [nm] distance for Coulomb cut-off
fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
when using PME
pme_order   = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol  = 1e-5  ; relative strength of
Ewald-shifted potential at rcoulomb

DispCorr = no


; Temperature coupling parameters
tcoupl= Nose-Hoover; Modified Berendsen thermostat
using velocity rescaling
tc-grps= DPPC SOL_Ion; Define groups to be coupled separately
to temperature bath
tau_t= 0.50.5; Group-wise coupling time constant (ps)
ref_t= 323323; Group-wise reference temperature (K)

; Pressure coupling parameters
pcoupl= Parrinello-Rahman; Pressure coupler used under NPT
conditions
pcoupltype= semiisotropic; Isotropic scaling in the x-y
direction, independent of the z direction
tau_p= 5.0; Coupling time constant (ps)
ref_p= 1.01.0; Reference pressure for coupling,
x-y, z directions (bar)
compressibility = 4.5e-54.5e-5; Isothermal compressibility
(bar^-1)

; Initial Velocity Generation
gen_vel= no; Velocity is read from the previous run
nstcomm= 1; COM removal frequency (steps)
comm_mode= Linear; Remove COM translation (linear / angular /
no)
comm_grps= DPPC SOL_Ion; COM removal relative to the specified
groups

; Parameters for treating bonded interactions
constraints= all-bonds; Which bonds/angles to constrain (all-bonds
/ hbonds / none / all-angles / h-angles)
constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE)
lincs_iter= 1; Number of iterations to correct for rotational
lengthening in LINCS (related to accuracy)
lincs_order= 4; Highest order in the expansion of the
constraint coupling matrix (related to accuracy)
continuation= no; Whether a fresh start or a continuation from
a previous run (yes/no)
--
Any suggestion would be helpful.

Thanks,
Tarak


On Mon, Feb 16, 2015 at 4:01 PM, tarak karmakar 
wrote:

> Oh! Thanks. :)
> Sorry I should have checked it before running the simulation.
> Now, I'm getting APL ~62.5 A^2 which is pretty good compared to the expt.
>
>
>
> On Sun, Feb 15, 2015 at 6:28 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 2/15/15 7:39 AM, tarak karmakar wrote:
>>
>>> Dear All,
>>> All atom simulation of DPPC bilayer (128 lipids) is resulting a low area
>>> per lipid (sliding down from ~58 to ~54 in 4 ns NPT).
>>> I'm performing the simulation in gromacs-5.0.4 with the charmm36 force
>>> field parameters for the lipid molecules. The NPT.mdp is pasted bellow,
>>>
>>>
>> We've been discussing this exact topic in another thread for days...
>>
>> Your .mdp settings are wrong.
>>
>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>>
>> -Justin
>>
>>
>>  
>>> -
>>> title= NPT production for cxcr_WT
>>> ; Parameters describing the details of the NVT simulation protocol
>>> integrator= md; Algorithm ("md" = molecular dynamics
>>> [leap-frog
>>> integrator]; "md-vv" = md using velocity verlet; sd = stochastic
>>> dynamics)
>>> dt   

Re: [gmx-users] Semiisotropic pressure coupling

[tarak karmakar]

Hi All,
Just read the thread and got some new information. I'm currently simulating
a pure DPPC bilayer with charmm36 lipid parameters in gromacs-5.0.4.
In doing so, I got a lower area per lipid (~0.56 nm^2) compared to the
experimental one (~0.63nm^2). The trajectory has run for ~3-4 ns. I have
used the following NPT.mdp file with the new set of cut-off schemes and a
time step of 2 fs.

--
title= NPT
integrator= md; Algorithm ("md" = molecular dynamics [leap-frog
integrator]; "md-vv" = md using velocity verlet; sd = stochastic dynamics)
dt= 0.002; Time-step (ps)
nsteps= 500; Number of steps to run (0.002 * 50 = 1 ns)

; Parameters controlling output writing
nstxout= 1 ; Write coordinates to output .trr file
every 2 ps
nstvout= 1 ; Write velocities to output .trr file every
2 ps
nstenergy= 1 ; Write energies to output .edr file every 2 ps
nstlog= 1000 ; Write output to .log file every 2 ps

; 7.3.9 Neighbor Searching
nstlist = 10; [steps] freq to update neighbor
list
ns_type = grid  ; method of updating neighbor list
pbc = xyz   ; periodic boundary conditions in
all directions

cutoff-scheme = Verlet

vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0


; 7.3.10 Electrostatics
coulombtype = PME   ; Particle-Mesh Ewald electrostatics
rcoulomb= 1.2   ; [nm] distance for Coulomb cut-off
fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
when using PME
pme_order   = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol  = 1e-5  ; relative strength of
Ewald-shifted potential at rcoulomb

DispCorr = no


; Temperature coupling parameters
tcoupl= Nose-Hoover; Modified Berendsen thermostat
using velocity rescaling
tc-grps= DPPC SOL_Ion; Define groups to be coupled separately
to temperature bath
tau_t= 0.50.5; Group-wise coupling time constant (ps)
ref_t= 323323; Group-wise reference temperature (K)

; Pressure coupling parameters
pcoupl= Parrinello-Rahman; Pressure coupler used under NPT
conditions
pcoupltype= semiisotropic; Isotropic scaling in the x-y
direction, independent of the z direction
tau_p= 5.0; Coupling time constant (ps)
ref_p= 1.01.0; Reference pressure for coupling,
x-y, z directions (bar)
compressibility = 4.5e-54.5e-5; Isothermal compressibility
(bar^-1)

; Initial Velocity Generation
gen_vel= no; Velocity is read from the previous run
nstcomm= 1; COM removal frequency (steps)
comm_mode= Linear; Remove COM translation (linear / angular /
no)
comm_grps= DPPC SOL_Ion; COM removal relative to the specified
groups

; Parameters for treating bonded interactions
constraints= all-bonds; Which bonds/angles to constrain (all-bonds
/ hbonds / none / all-angles / h-angles)
constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE)
lincs_iter= 1; Number of iterations to correct for rotational
lengthening in LINCS (related to accuracy)
lincs_order= 4; Highest order in the expansion of the
constraint coupling matrix (related to accuracy)
continuation= no; Whether a fresh start or a continuation from
a previous run (yes/no)
--
Any comment on this?

Thanks and regards,
Tarak







On Tue, Feb 17, 2015 at 5:52 AM, shivangi nangia 
wrote:

> Hello Justin,
>
> I have a follow up question.
>
> The non-bonded parameters you have pointed out to :
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> is valid if the system contains only lipid or it should be use with a
> system containing lipid and protein too.
>
> Thanks,
>
> sxn
>
>
> On Mon, Feb 16, 2015 at 2:10 PM, shivangi nangia <
> shivangi.nan...@gmail.com>
> wrote:
>
> > Thanks a lot Justin!!!
> >
> >
> >
> >
> >
> >
> > On Sun, Feb 15, 2015 at 1:13 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 2/15/15 1:02 PM, shivangi nangia wrote:
> >>
> >>> Dear Justin,
> >>>
> >>> Thanks for the continuous help.
> >>>
> >>> Since I have done reverse CG, The CG POPC was equilibrated alone
> >>> anisotropically, The APL was fine there.
> >>> On reverse CG and NVT its still fine, it only after NPT it starts
> >>> dropping.
> >>>
> >>>
> >> Of course it's fine during NVT - the box can't change so the area is
> >> constant.
> >>
> >>  I am calculating APL as (2*Lx*Ly)/(No. of Lipids).
> >>>