date:20181110

Re: [gmx-users] Unable to generate .rtp file from gro and pdb file.

2018-11-10 Thread Mark Abraham

Hi,

Does your input conformation + topology work for a single molecule of this
type?

Mark

On Sun, Nov 11, 2018 at 1:08 AM Karpurmanjari Kakati <
ch18resch01...@iith.ac.in> wrote:

> Hi
> I tried doing the same, like you said.
> 1. Copied the OPLS AA force field files to the directory, where my pdb
> files were present.
> 2. Modified the rtp file. but the error comes up in the pdb2gmx "no
> residjue type in the residue database. "
> Alternatively, what I tired doing is the following:
>
> 1. I constructed the polymer in Avogrado software.
> 2. Used OBGMX to make the itp file. But the charge column genereated by
> OBGMX is .
> 3. To include charge, I went back to Avogrado, and took the charges from
> each atom and included it in the itp file by replacing the   against
> each atom.
> 4. Now my topology file looks something like this:
>
>
>
> #include "oplsaa.ff/forcefield.itp"
>
>
>
> [ atomtypes ]
> ; name1 name2   mass charge  ptype   sigma   epsilon
> N_3  N_314.0067  0.227A  0.3261   0.2889
> C_3  C_312.0107  0.050   A  0.3431   0.4396
> C_2  C_212.0107  0.261  A  0.3431   0.4396
> O_2  O_215.9994  -0.013   A  0.3118   0.2512
> N_2  N_214.0067  -0.302   A  0.3261   0.2889
> N_R  N_R14.0067  -0.289   A  0.3261   0.2889
> O_3  O_315.9994  -0.390A  0.3118   0.2512
> H_   H_  1.0079  0.200  A  0.2571   0.1842
> NE  NE14.0067  0.227   A  0.3261   0.2889
> NH1  NH114.0067  0.227   A  0.3261   0.2889
> NH2  NH214.0067  0.227   A  0.3261   0.2889
>
> CA  CA12.0107  0.050   A  0.3431   0.4396
> C  C12.0107  0.050  A  0.3431   0.4396
> CB  CB12.0107  0.261   A  0.3431   0.4396
> CG  CG12.0107  0.261   A  0.3431   0.4396
> CD  CD12.0107 0.261   A  0.3431   0.4396
> CZ  CZ12.0107  0.261   A  0.3431   0.4396
> N   N14.0067  0.227A  0.3261   0.2889
> H1   H1  1.0079  0.200   A  0.2571   0.1842
> H2   H2  1.0079  0.200   A  0.2571   0.1842
> HA   HA  1.0079 0.200   A  0.2571   0.1842
> HB1   HB1  1.0079  0.200   A  0.2571   0.1842
> HB2   HB2  1.0079  0.200   A  0.2571   0.1842
> HB3   HB3  1.0079  0.200   A  0.2571   0.1842
> H   H  1.0079  0.200   A  0.2571   0.1842
> HA1   HA1  1.0079  0.200   A  0.2571   0.1842
> HA2   HA2  1.0079  0.200   A  0.2571   0.1842
> HG1   HG1  1.0079  0.200   A  0.2571   0.1842
> HG2   HG2  1.0079  0.200   A  0.2571   0.1842
> HD1   HD1  1.0079  0.200   A  0.2571   0.1842
> HD2   HD2  1.0079  0.200   A  0.2571   0.1842
> HE   HE  1.0079  0.200   A  0.2571   0.1842
> HH21   HH21  1.0079  0.200   A  0.2571   0.1842
> HH22   HH22  1.0079  0.200   A  0.2571   0.1842
> HH11   HH11  1.0079  0.200   A  0.2571   0.1842
> HH12   HH12  1.0079  0.200   A  0.2571   0.1842
> HG   HG  1.0079  0.200   A  0.2571   0.1842
> HD   HD  1.0079  0.200   A  0.2571   0.1842
> HW1   HW1  1.0079 0.200   A  0.2571   0.1842
> HW2  HW2  1.0079  0.200   A  0.2571   0.1842
> O  O15.9994 -0.390   A  0.3118   0.2512
>
>
>
> #include 
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre-gel.itp"
> #endif
>
> #include 
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre-pe.itp"
> #endif
>
> [ system ]
> GEL and PE
>
> [ molecules ]
> GEL  5
> PE   2
>
>
>
> And now I am performing EM in vacuum for the system. The error comes to be
> it stops Energy minimization before the desired energy is reached.
> Like I read from other error mails, it says the topology or the itp file
> had defects.
>
>
> My query is, I just added charges to the itp file generated from OBGMX.
> Is that the reason why my energy minimization is stopping at the middle.
>
> Kindly help with this.
>
>
> Karpurmanjari
>
>
>
>
>
>
>
>
>
>
> On Mon, Nov 5, 2018 at 10:46 PM Karpurmanjari Kakati <
> ch18resch01...@iith.ac.in> wrote:
>
> > Dear Justin,
> >
> > I want to add the residue "hydroxyproline" or "HYP" in the OPLS AA in the
> > aminoacids.rtp file . I have all the files of OPLS AA force field in my
> > working directory.
> > For that I tried to generate the initial rtp format file from the hydroxy
> > proline's .pdb

Re: [gmx-users] LINCS warning

2018-11-10 Thread Mark Abraham

Hi,

That tends to suggest either your ligand conformation or ligand parameters
are not appropriate. What happens with ligand in vacuo with EM and then NVE
with a very small time step, e.g. 0.5 ps?

Mark

On Sat, Nov 10, 2018 at 10:50 AM Farial Tavakoli 
wrote:

> Dear gromacs users
>
> I am trying to simulate a complex, including a protein and a peptidec
> ligand with 2 phosphotyrosine residues.
> The protein topology was generated using amber99sb.ff in gromacs and the
> ligand topology was generated using ff99sb in amber tools 16, then the
> .inpcrd and .prmtop files were converted to .gmx and .top files using
> acpype python script.
> *python acpype.py -p prmtop -x inpcrd*
> .itp file was created by removing  header and footer of .top file.
> Then .gro and .top files were modified according to the tutorial in
> gromacs.
> I tryed to minimize the complex , but it stoped before 100 steps :
>
>
>
>
>
> *Steepest Descents converged to machine precision in 80 steps,but did not
> reach the requested Fmax < 1000.Potential Energy  = -6.5639856e+05Maximum
> force =  7.0647156e+04 on atom 5256Norm of force =  5.8775842e+02*
>
> and when I run NVT simulation , faced to LINCS warning:
>
>
>
>
>
>
>
>
>
>
> *starting mdrun 'Protein in water'20 steps,400.0 ps.step 0Step 5,
> time 0.01 (ps)  LINCS WARNINGrelative constraint deviation after LINCS:rms
> 0.016999, max 0.734404 (between atoms 5258 and 5261)bonds that rotated more
> than 30 degrees: atom 1 atom 2  angle  previous, current, constraint
> length   5258   5261   90.00.0960   0.1665  0.0960   5283   5286
> 90.00.0960   0.1425  0.0960Wrote pdb files with previous and
> current coordinates*
> I separated my complex in to protein and ligand and simulated the protein
> alone in the TIP3P water model. that was stable. then, simulated the ligand
> in vacuo and faced with LINCS warning.
> Both force fields that were used to generate topologies were AMBER99sb, Is
> it possible its because of .mdp files which I used?
> Would you please reply and advice me how I can resolve this problem?
>
> best regards
> Farial
>
> the em.mdp file:
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator  = steep
> emtol   = 1000.0
> emstep  = 0.01
> nsteps  = 5
> nstlist = 1
> cutoff-scheme   = Verlet
> ns_type = grid
> coulombtype = PME
> rcoulomb= 1.0
> rvdw= 1.0
> pbc = xyz
>
> nvt.mdp file:
> title   = AMBER  NVT equilibration
> define  = -DPOSRES  ; position restrain the protein
> ; Run parameters
> integrator  = md
> nsteps  = 20 ; 2 * 20 = 400 ps
> dt  = 0.002
> ; Output control
> nstxout = 500
> nstvout = 500
> nstenergy   = 500
> nstlog  = 500
> ; Bond parameters
> continuation= no
> constraint_algorithm= lincs
> constraints = h-bonds
> lincs_iter  = 1
> lincs_order = 4
> ; Nonbonded settings
> cutoff-scheme   = Verlet
> ns_type = grid
> nstlist = 10
> rcoulomb= 1.0
> rvdw= 1.0
> ; Electrostatics
> coulombtype = PME
> pme_order   = 4
> fourierspacing  = 0.16
> ; Temperature coupling is on
> tcoupl  = V-rescale
> tc-grps = Protein Non-Protein
> tau_t   = 0.1 0.1
> ref_t   = 300 300
> ; Pressure coupling is off
> pcoupl  = no
> ; Periodic boundary conditions
> pbc = xyz
> ; Velocity generation
> gen_vel = yes
> gen_temp= 300
> gen_seed= -1
> --
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Re: [gmx-users] Vacuum simulation of a peptide feasible using GROMACS?

2018-11-10 Thread Mark Abraham

Yes.

On Fri, Nov 9, 2018 at 9:55 PM Neena Susan Eappen <
neena.susaneap...@mail.utoronto.ca> wrote:

> Hello GROMACS users,
>
>
> I am a first time user of GROMACS. I was wondering can I model a peptide
> (to learn about secondary structure) in gas phase with different charge
> sites using GROMACS?
>
>
> Many thanks,
>
>
> Neena Eappen
> Graduate Student
> Jockusch Lab, U of T
> --
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Re: [gmx-users] Mpirun continuing mdrun

2018-11-10 Thread Mark Abraham

Hi,

No, your log file has information on whatever might be the problem. I would
start by investigating what warning you are suppressing. Those are not
given just for fun :-)

mark

On Sun, Nov 11, 2018 at 12:23 AM rose rahmani  wrote:

> Hi,
>
> I did 2ns simulation as an equilibration step by mdrun,
>
> Mdrun -v -deffnm md1
>
> and now i want to do product run for 100ns by mpirun,
>
> Grompp -p -f -c md1.gro -t md1.cpt -o md2.tpr -maxwarn 1
>
> Mpirun -np 8 mdrun -v -deffnm md2
>
> but it will crush after few minutes at intialization...
> Is that because i use mpirun?
>
> Best
> Rose
> --
> Gromacs Users mailing list
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> * Please search the archive at
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>
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Re: [gmx-users] Unable to generate .rtp file from gro and pdb file.

2018-11-10 Thread Karpurmanjari Kakati

Hi
I tried doing the same, like you said.
1. Copied the OPLS AA force field files to the directory, where my pdb
files were present.
2. Modified the rtp file. but the error comes up in the pdb2gmx "no
residjue type in the residue database. "
Alternatively, what I tired doing is the following:

1. I constructed the polymer in Avogrado software.
2. Used OBGMX to make the itp file. But the charge column genereated by
OBGMX is .
3. To include charge, I went back to Avogrado, and took the charges from
each atom and included it in the itp file by replacing the   against
each atom.
4. Now my topology file looks something like this:



#include "oplsaa.ff/forcefield.itp"



[ atomtypes ]
; name1 name2   mass charge  ptype   sigma   epsilon
N_3  N_314.0067  0.227A  0.3261   0.2889
C_3  C_312.0107  0.050   A  0.3431   0.4396
C_2  C_212.0107  0.261  A  0.3431   0.4396
O_2  O_215.9994  -0.013   A  0.3118   0.2512
N_2  N_214.0067  -0.302   A  0.3261   0.2889
N_R  N_R14.0067  -0.289   A  0.3261   0.2889
O_3  O_315.9994  -0.390A  0.3118   0.2512
H_   H_  1.0079  0.200  A  0.2571   0.1842
NE  NE14.0067  0.227   A  0.3261   0.2889
NH1  NH114.0067  0.227   A  0.3261   0.2889
NH2  NH214.0067  0.227   A  0.3261   0.2889

CA  CA12.0107  0.050   A  0.3431   0.4396
C  C12.0107  0.050  A  0.3431   0.4396
CB  CB12.0107  0.261   A  0.3431   0.4396
CG  CG12.0107  0.261   A  0.3431   0.4396
CD  CD12.0107 0.261   A  0.3431   0.4396
CZ  CZ12.0107  0.261   A  0.3431   0.4396
N   N14.0067  0.227A  0.3261   0.2889
H1   H1  1.0079  0.200   A  0.2571   0.1842
H2   H2  1.0079  0.200   A  0.2571   0.1842
HA   HA  1.0079 0.200   A  0.2571   0.1842
HB1   HB1  1.0079  0.200   A  0.2571   0.1842
HB2   HB2  1.0079  0.200   A  0.2571   0.1842
HB3   HB3  1.0079  0.200   A  0.2571   0.1842
H   H  1.0079  0.200   A  0.2571   0.1842
HA1   HA1  1.0079  0.200   A  0.2571   0.1842
HA2   HA2  1.0079  0.200   A  0.2571   0.1842
HG1   HG1  1.0079  0.200   A  0.2571   0.1842
HG2   HG2  1.0079  0.200   A  0.2571   0.1842
HD1   HD1  1.0079  0.200   A  0.2571   0.1842
HD2   HD2  1.0079  0.200   A  0.2571   0.1842
HE   HE  1.0079  0.200   A  0.2571   0.1842
HH21   HH21  1.0079  0.200   A  0.2571   0.1842
HH22   HH22  1.0079  0.200   A  0.2571   0.1842
HH11   HH11  1.0079  0.200   A  0.2571   0.1842
HH12   HH12  1.0079  0.200   A  0.2571   0.1842
HG   HG  1.0079  0.200   A  0.2571   0.1842
HD   HD  1.0079  0.200   A  0.2571   0.1842
HW1   HW1  1.0079 0.200   A  0.2571   0.1842
HW2  HW2  1.0079  0.200   A  0.2571   0.1842
O  O15.9994 -0.390   A  0.3118   0.2512



#include 

; Include Position restraint file
#ifdef POSRES
#include "posre-gel.itp"
#endif

#include 

; Include Position restraint file
#ifdef POSRES
#include "posre-pe.itp"
#endif

[ system ]
GEL and PE

[ molecules ]
GEL  5
PE   2



And now I am performing EM in vacuum for the system. The error comes to be
it stops Energy minimization before the desired energy is reached.
Like I read from other error mails, it says the topology or the itp file
had defects.


My query is, I just added charges to the itp file generated from OBGMX.
Is that the reason why my energy minimization is stopping at the middle.

Kindly help with this.


Karpurmanjari










On Mon, Nov 5, 2018 at 10:46 PM Karpurmanjari Kakati <
ch18resch01...@iith.ac.in> wrote:

> Dear Justin,
>
> I want to add the residue "hydroxyproline" or "HYP" in the OPLS AA in the
> aminoacids.rtp file . I have all the files of OPLS AA force field in my
> working directory.
> For that I tried to generate the initial rtp format file from the hydroxy
> proline's .pdb and .gro  files using the following command:
> gmx x2top  -f hyd.gro  -r hyd.rtp  -pbc -ff oplsaa
>
> and I got the following error:
>
> Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t
> There are 23 name to type translations in file oplsaa.ff
> Generating bonds from distances...
> atom 18
> Can not find forcefield for atom CA-2 with 4 bonds
> Can not find forcefield

[gmx-users] Mpirun continuing mdrun

2018-11-10 Thread rose rahmani

Hi,

I did 2ns simulation as an equilibration step by mdrun,

Mdrun -v -deffnm md1

and now i want to do product run for 100ns by mpirun,

Grompp -p -f -c md1.gro -t md1.cpt -o md2.tpr -maxwarn 1

Mpirun -np 8 mdrun -v -deffnm md2

but it will crush after few minutes at intialization...
Is that because i use mpirun?

Best
Rose
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[gmx-users] LINCS warning

2018-11-10 Thread Farial Tavakoli

Dear gromacs users

I am trying to simulate a complex, including a protein and a peptidec
ligand with 2 phosphotyrosine residues.
The protein topology was generated using amber99sb.ff in gromacs and the
ligand topology was generated using ff99sb in amber tools 16, then the
.inpcrd and .prmtop files were converted to .gmx and .top files using
acpype python script.
*python acpype.py -p prmtop -x inpcrd*
.itp file was created by removing  header and footer of .top file.
Then .gro and .top files were modified according to the tutorial in
gromacs.
I tryed to minimize the complex , but it stoped before 100 steps :





*Steepest Descents converged to machine precision in 80 steps,but did not
reach the requested Fmax < 1000.Potential Energy  = -6.5639856e+05Maximum
force =  7.0647156e+04 on atom 5256Norm of force =  5.8775842e+02*

and when I run NVT simulation , faced to LINCS warning:










*starting mdrun 'Protein in water'20 steps,400.0 ps.step 0Step 5,
time 0.01 (ps)  LINCS WARNINGrelative constraint deviation after LINCS:rms
0.016999, max 0.734404 (between atoms 5258 and 5261)bonds that rotated more
than 30 degrees: atom 1 atom 2  angle  previous, current, constraint
length   5258   5261   90.00.0960   0.1665  0.0960   5283   5286
90.00.0960   0.1425  0.0960Wrote pdb files with previous and
current coordinates*
I separated my complex in to protein and ligand and simulated the protein
alone in the TIP3P water model. that was stable. then, simulated the ligand
in vacuo and faced with LINCS warning.
Both force fields that were used to generate topologies were AMBER99sb, Is
it possible its because of .mdp files which I used?
Would you please reply and advice me how I can resolve this problem?

best regards
Farial

the em.mdp file:
; minim.mdp - used as input into grompp to generate em.tpr
integrator  = steep
emtol   = 1000.0
emstep  = 0.01
nsteps  = 5
nstlist = 1
cutoff-scheme   = Verlet
ns_type = grid
coulombtype = PME
rcoulomb= 1.0
rvdw= 1.0
pbc = xyz

nvt.mdp file:
title   = AMBER  NVT equilibration
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md
nsteps  = 20 ; 2 * 20 = 400 ps
dt  = 0.002
; Output control
nstxout = 500
nstvout = 500
nstenergy   = 500
nstlog  = 500
; Bond parameters
continuation= no
constraint_algorithm= lincs
constraints = h-bonds
lincs_iter  = 1
lincs_order = 4
; Nonbonded settings
cutoff-scheme   = Verlet
ns_type = grid
nstlist = 10
rcoulomb= 1.0
rvdw= 1.0
; Electrostatics
coulombtype = PME
pme_order   = 4
fourierspacing  = 0.16
; Temperature coupling is on
tcoupl  = V-rescale
tc-grps = Protein Non-Protein
tau_t   = 0.1 0.1
ref_t   = 300 300
; Pressure coupling is off
pcoupl  = no
; Periodic boundary conditions
pbc = xyz
; Velocity generation
gen_vel = yes
gen_temp= 300
gen_seed= -1
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Re: [gmx-users] GROMACS 2018.3 ansible playbook for wget, extract, build, install

2018-11-10 Thread Benson Muite

Hi Darin,

Easybuild (https://easybuilders.github.io/easybuild/):
https://github.com/easybuilders/easybuild-easyblocks/blob/master/easybuild/easyblocks/g/gromacs.py
Spack (https://github.com/spack/spack):
https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/gromacs/package.py

A bit of searching found the following which can likely be updated to
latest versions:
Ansible playbook:
https://github.com/LIP-Computing/ansible-role-gromacs
Docker file:
https://github.com/soellman/gromacs/blob/master/Dockerfile
Nvidia provided docker/singularity image:
https://ngc.nvidia.com/registry/hpc-gromacs
Forked from Intel singularity repository:
https://github.com/luco2018/Intel-HPC-Container/tree/master/containers/gromacs

It would be useful to know what you choose to use.

Regards,
Benson


On 11/9/18 7:00 PM, Benson Muite wrote:
> There is also an rpm:
>
> https://centos.pkgs.org/7/epel-x86_64/gromacs-2018.2-1.el7.x86_64.rpm.html
>
> for other versions see:
>
> https://pkgs.org/download/gromacs
>
> On 11/9/18 6:54 PM, Benson Muite wrote:
>> The installation instructions 
>> (http://manual.gromacs.org/documentation/2018/install-guide/index.html) make 
>> it possible to write a simple shell script - though optmizing may require a 
>> few more tests. For example to install a basic configuration in 
>> $HOME/gromacs use
>>
>> wget 
>> ftp.gromacs.org/pub/gromacs/gromacs-2018.3.tar.gz
>> tar xfz gromacs-2018.3.tar.gz
>> cd gromacs-2018.3
>> mkdir build
>> cd build
>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON 
>> -DCMAKE_INSTALL_PREFIX=$HOME/gromacs
>> make
>> make check
>> sudo make install
>> source $HOME/gromacs/bin/GMXRC
>>
>> On 11/9/18 5:59 PM, Darin Lory-External wrote:
>> To distribution,
>>
>> Does anybody have a GROMACS 2018.3 (or any version) ansible playbook for 
>> wget, extract, build, install or even a nice shell script for Linux (RHEL, 
>> but I can convert other linuxes)
>>
>> Darin S Lory
>> Email: darin.l...@regeneron.com
>>
>>

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