[gmx-users] Concrete pull code explanation needed

[Du, Yu]

Dear Justin and gmx users, 


I have gone through mdp-option and Justin A. Lemkul's COM pulling tutorial 
serveral times.


The following is Justin's pull code.


; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A 
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups= 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0


My understanding lists as follows, 


Justin defines two pull groups, with `pull-ngroups = 2`, each of them has a 
name in the index.ndx generated by `gmx make_ndx -f npt.gro`and their names are 
defined by `pull_group1_name = Chain_B` and `pull_group2_name = Chain_A`.


My question is about the definition of pulling coordination and the orientation 
of pulling force.


1) I learnt from [gmx-users] Change to umbrella sampling pull code，
"You need: pull-coord1-groups = 1 2 otherwise the reaction coordinate is 
undefined, or otherwise defaults to the entire system, I can't remember which. 
-Justin"


I know it's a plot :) in the input.pdb that proteins are placed exquisitely 
along the z-axis which is the same as the pulling coordinate but it makes pull 
code confused and here I need a concrete explanation.
1.The pull coordinate is the line that connects COM of group1 and group2 with 
`pull_coord1_groups= 1 2`. 
OR 2. The pull coordinate is the z axis with `pull_coord1_dim = N N Y`. 
Which is correct? 


2)Then turn to the orientation of pulling forces.
My understanding is that force1 acts on pull_group1, force2 acts on pull_group2 
and the orientation of force 1 and 2 is opposite, both forces have a rate of 
10nm per ns. 
Is my understanding and the below schematic draw right?


Z-axis-0-5--->---positive-orientation--->-25-->
   


The last question is about the umbrella sampling.
I learnt from [gmx-users] Re: doubt about your Umbrella Sampling tutorial that 
it's ok to remove the pores of Chain B during the US. But in longer simulation 
time and in the periodical box, will the COM of Chain B and A be affacted by 
the boundary? and then affact the calculation of US potential?


Best Regards, 
Yu


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[gmx-users] ligan minimization in vacuo

[‪farial tavakoli‬ ‪]

Dear gmx-users
I have a problem in equilibration my protein-ligand complex and encountered to 
this error after 2 steps of 5 steps:one or more water molecules can not be 
settled. check for bad contacts or reduce the time steps. 
so I decided to create a topology for my designed drug (50 atoms) as a ligand 
to minimize it in the vacuo in the absence of the protein to check if it 
minimizes  , so i tried to change the .itp file obtained from PRODRG to create 
a .top file,  in this way:I added  " ; Include forcefield parameters
    #include "gromos43a1.ff/forcefield.itp " above the [ moleculetype ] 
directive as a first line , then added [ system ] and [ molecule ] directives 
under the ligand, respectively :
  23  24  26  27   1    180.0   33.5 2    180.0   33.5 2 ; dih   CAS  CAR  NAQ  
CAN   
  32  27  26  24   1    180.0   33.5 2    180.0   33.5 2 ; dih   CAM  CAN  NAQ  
CAR   
  39  37  36  30   1    180.0    5.9 2    180.0    5.9 2 ; dih   SAG  CAH  CAK  
CAP   
  40  48  49  50   1    180.0    7.1 2    180.0    7.1 2 ; dih   CAA  CAF  OAJ  
HAJ

; Ligand position restraints
#ifdef POSRES
#include "posre_DRG.itp"
#endif

; Include water topology
#include "gromos43a1.ff/spc.itp"

[ system ]
; Name
DRG in water

[ molecules ]
; Compound    #mols
DRG          1
issued this command:gmx grompp -v -f em.mdp -c DRG.gro -p DRG.top -o 
DRG-EM-vacuum.tprgmx mdrun -v -deffnm DRG-EM-vacuum -c DRG-EM-vacuum.gro 
and simulation results:
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps    =    5
Step=    0, Dmax= 1.0e-02 nm, Epot=  1.41636e+03 Fmax= 2.81150e+04, atom= 25
Step=    1, Dmax= 1.0e-02 nm, Epot=  1.01416e+03 Fmax= 1.21118e+04, atom= 25
Step=    2, Dmax= 1.2e-02 nm, Epot=  7.87016e+02 Fmax= 4.71639e+03, atom= 25
Step=    3, Dmax= 1.4e-02 nm, Epot=  6.94638e+02 Fmax= 5.88719e+03, atom= 15
Step=    5, Dmax= 8.6e-03 nm, Epot=  6.79808e+02 Fmax= 7.13390e+03, atom= 15
Step=    7, Dmax= 5.2e-03 nm, Epot=  6.29169e+02 Fmax= 1.31714e+03, atom= 25
Step=    8, Dmax= 6.2e-03 nm, Epot=  6.12279e+02 Fmax= 2.91712e+03, atom= 14
Step=   10, Dmax= 3.7e-03 nm, Epot=  6.04849e+02 Fmax= 2.77294e+03, atom= 27
Step=   12, Dmax= 2.2e-03 nm, Epot=  5.86062e+02 Fmax= 9.77798e+02, atom= 24

writing lowest energy coordinates.

Back Off! I just backed up DRG-EM-vacuum.gro to ./#DRG-EM-vacuum.gro.1#

Steepest Descents converged to Fmax < 1000 in 13 steps
Potential Energy  =  5.8606232e+02
Maximum force =  9.7779791e+02 on atom 24
Norm of force =  3.8248090e+02

Simulation ended prematurely, no performance report will be written.


 here's my em.mdp file:

integrator      = steep        ; Algorithm (steep = steepest descent 
minimization)
emtol            = 1000.0      ; Stop minimization when the maximum force < 
10.0 kJ/mol
emstep     = 0.01     ; Energy step size
nsteps          = 5       ; Maximum number of (minimization) steps to 
perform
energygrps    = system    ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist               = 1            ; Frequency to update the neighbor list 
and long range forces
cutoff-scheme   = Verlet
ns_type            = grid        ; Method to determine neighbor list (simple, 
grid)
rlist                  = 1.0        ; Cut-off for making neighbor list (short 
range forces)
coulombtype = PME  ; Treatment of long range electrostatic interactions
rcoulomb          = 1.0        ; long range electrostatic cut-off
rvdw                = 1.0        ; long range Van der Waals cut-off
pbc         = xyz        ; Periodic Boundary Conditions

I just wanted to know if I did correct?In addition after minimization in vacuo 
, checked my ligand in pymol and noticed it is disintegrated.  Is there anyone 
help me how come it is disintegrated ,however i edited the .itp file obtained 
from PRODRG ( charges and charg groups)? How can i fix this problem to 
equilibrate my complex? 


 thank you in advance 
Farial
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[gmx-users] Help on MD performance, GPU has less load than CPU.

[Davide Bonanni]

Hi,

I am working on a node with Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz, 16
physical core, 32 logical core and 1 GPU NVIDIA GeForce GTX 980 Ti.
I am launching a series of 2 ns molecolar dynamics simulations of a system
of 6 atoms.
I tried diverse setting combination, but however i obtained the best
performance with the command:

"gmx mdrun  -deffnm md_LIG -cpt 1 -cpo restart1.cpt -pin on"

which use 32 OpenMP threads, 1 MPI thread, and the GPU.
At the end of the file.log of molecular dynamic production I obtain this
message:

"NOTE: The GPU has >25% less load than the CPU. This imbalance causes
  performance loss."

I don't know how can improve the load on CPU more than this, or how I can
decrease the load on GPU. Do you have any suggestions?

Thank you in advance.

Cheers,

Davide Bonanni


Initial and final part of LOG file here:

Log file opened on Sun Jul  9 04:02:44 2017
Host: bigblue  pid: 16777  rank ID: 0  number of ranks:  1
   :-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:



GROMACS:  gmx mdrun, VERSION 5.1.4
Executable:   /usr/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -deffnm md_fluo_7 -cpt 1 -cpo restart1.cpt -pin on

GROMACS version:VERSION 5.1.4
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:enabled
OpenCL support: disabled
invsqrt routine:gmx_software_invsqrt(x)
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.4-sse2-avx
RDTSCP usage:   enabled
C++11 compilation:  disabled
TNG support:enabled
Tracing support:disabled
Built on:   Tue  8 Nov 12:26:14 CET 2016
Built by:   root@bigblue [CMAKE]
Build OS/arch:  Linux 3.10.0-327.el7.x86_64 x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
Build CPU family:   6   Model: 63   Stepping: 2
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /bin/cc GNU 4.8.5
C compiler flags:-march=core-avx2-Wextra
-Wno-missing-field-initializers
-Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value
-Wunused-parameter  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
 -Wno-array-bounds
C++ compiler:   /bin/c++ GNU 4.8.5
C++ compiler flags:  -march=core-avx2-Wextra
-Wno-missing-field-initializers
-Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast  -Wno-array-bounds
Boost version:  1.55.0 (internal)
CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on
Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44
CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=
compute_30,code=sm_30;-gencode;arch=compute_35,code=
sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=
compute_50,code=sm_50;-gencode;arch=compute_52,code=
sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=
compute_61,code=sm_61;-gencode;arch=compute_60,code=
compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;;
;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-
Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-
fexcess-precision=fast;-Wno-array-bounds;
CUDA driver:8.0
CUDA runtime:   8.0


Running on 1 node with total 16 cores, 32 logical cores, 1 compatible GPU
Hardware detected:
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
Family:  6  model: 63  stepping:  2
CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX2_256
  GPU info:
Number of GPUs detected: 1
#0: NVIDIA GeForce GTX 980 Ti, compute cap.: 5.2, ECC:  no, stat:
compatible



Changing nstlist from 20 to 40, rlist from 1.2 to 1.2

Input Parameters:
   integrator = sd
   tinit  = 0
   dt = 0.002
   nsteps = 100
   init-step  = 0
   simulation-part= 1
   comm-mode  = Linear
   nstcomm= 100
   bd-fric= 0
   ld-seed= 57540858
   emtol  = 10
   emstep = 0.01
   niter  = 20
   fcstep = 0
   nstcgsteep = 1000
   nbfgscorr  = 10
   rtpi   = 0.05
   nstxout  

Re: [gmx-users] Acetonitrile using CHARMM ff

[Sonia Milena Aguilera Segura]

Dear Justin, 

Thank you for the answer. I changed the two parameters suggested in the mdp 
file and I ran again a minimization, 200 ps NVT, 200 ps NPT, and 1 ns MD for 
the two cases of the previous mail, and now I am getting densities around 771 
g/m3 which is slightly underestimated, but close to what other authors have 
obtained (774 others and 777 experimental). Also, I got slightly higher values 
for dielectric constants and diffusivities, also closer to another simulation 
with CHARMM. The energies also changed, but I guess that was expected. It looks 
like reproducing the dielectric constant with the current parameters is not 
possible. Is there anything that can be changed in order to get a better 
description? In terms of simulation, what is the dielectric constant depending 
of?

Moreover, I observed that this time I got lower values for P during the NPT 
equilibration, but still is too far from 1 bar.  I really don't understand why 
for the NVT simulation I get a T around 298, but as soon as I turn on the 
pcoupl, the T rises to 300-301 K and the P gets average values of 7 and 4 bar 
(vs 8 and 14 for the previous simulations). Then at the end of the 1-ns MD the 
temperature remains around 301 and the P is -1 and 2.7 bar. Considering the 
parameters I am using, is there anything I can change to make the P coupling 
better? I am running a 3 nm box with 308 molecules. This is the full mdp file:

; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.0005
nsteps   = 200   ; 1 ns
nstcomm  = 100
;energygrps  = non-Water
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= verlet
nstlist  = 20
ns_type  = grid
pbc  = xyz
rlist= 1.2
; Electrostatics
coulombtype  = PME
rcoulomb = 1.2
; van der Waals
vdwtype  = cutoff
vdw-modifier = force-switch
rvdw-switch  = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = no
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 298.15
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman 
tau_p= 1.0
compressibility  = 4.5e-05
ref_p= 1.0 
; Do not generate velocities
gen_vel  = no 
; options for bonds
constraints  = none  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Constrain the starting configuration
; since we are continuing from NPT
continuation = yes 
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12


Thank you very much, 

Sonia Aguilera
PhD student
ENSCM
> ; Run control
> integrator   = sd   ; Langevin dynamics
> tinit= 0
> dt   = 0.0005
> nsteps   = 4000   ; 20 ns
> nstcomm  = 100
> ; Neighborsearching and short-range nonbonded interactions
> cutoff-scheme= verlet
> nstlist  = 20
> ns_type  = grid
> pbc  = xyz
> rlist= 1.2
> ; Electrostatics
> coulombtype  = PME
> rcoulomb = 1.2
> ; van der Waals
> vdwtype  = cutoff
> vdw-modifier = potential-switch
> rvdw-switch  = 1.0
> rvdw = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr  = EnerPres

CHARMM uses a force switch, and only apply dispersion correction in the case of 
lipid monolayers.

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

-Justin

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Re: [gmx-users] Invalid order for directive X

[Mark Abraham]

Hi,

The output files from acpype I mean.

Mark

On Mon, Jul 10, 2017 at 3:59 PM Khadija Amine  wrote:

> Hi Mark,
>
> Thank you for your quick reply.
>
> You mean by 'the acpype files must be edited to have all the atom types in
> a block before any of the molecules' all the files with GMX as I have used
> amberff99sb.
>
> There are many files for charmm, opls, ...
>
> In my case, I should see the following files: ACT_GMX.gro. ACT_GMX.itp,
> ACT_NEW.pdb ?
>
> Khadija
>
>
> *​Khadija Amine*
> Ph.D. Biology and Health
> Biochemistry & Bioinformatics
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[gmx-users] Invalid order for directive X

[Khadija Amine]

Hi Mark,

Thank you for your quick reply.

You mean by 'the acpype files must be edited to have all the atom types in
a block before any of the molecules' all the files with GMX as I have used
amberff99sb.

There are many files for charmm, opls, ...

In my case, I should see the following files: ACT_GMX.gro. ACT_GMX.itp,
ACT_NEW.pdb ?

Khadija


*​Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
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Re: [gmx-users] Regarding terminal residue parameters (Capping)

[Harry Mark Greenblatt]

BS”D



I am trying to simulate a multichain amino acid structure. PDB ID 2BEG.

I am experiencing problems with the C and N terminal residues i. e. C-ALA
and N-LEU.

An abnormal non-bonded interaction keeps forming between atoms C from ALA42
and N from LEU17.

Do you mean from Ala42 of Chain A to Leu17 of Chain B?

If the chain specifiers are intact in the pdb input file then no bond should be 
formed.  What does the  output of pdb2gmx say?

Harry


Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel

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Re: [gmx-users] error in NVT run

[Hermann, Johannes]

Hello Aman,

this probably means that your system is not well equilibrated. You can 
try a smaller time step. But I would also recommend to google the error 
and you will find a lot of qualified suggestions.


All the best

Johannes


On 10.07.2017 14:33, Aman Deep wrote:

hello,

I was trying to simulate a protein of 1200 residues, during NVT run I got
error repeatedly that is:

*step 11: Water molecule starting at atom 115665 can not be settled.*
*Check for bad contacts and/or reduce the timestep if appropriate.*

please tell me what is reason for it and how to solve it??

thank you


--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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[gmx-users] error in NVT run

[Aman Deep]

hello,

I was trying to simulate a protein of 1200 residues, during NVT run I got
error repeatedly that is:

*step 11: Water molecule starting at atom 115665 can not be settled.*
*Check for bad contacts and/or reduce the timestep if appropriate.*

please tell me what is reason for it and how to solve it??

thank you
-- 
Aman Deep
MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025
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Re: [gmx-users] Can't locate state.cpt for gmx mdrun

[Mark Abraham]

Hi,

Checkpoints continue unfinished calculations. Energy minimization generally
is short, and only stops when complete, so there is no meaningful restart.

Mark

On Mon, 10 Jul 2017 00:13 Yonatan Zelnik  wrote:

> Hello Justin,
>
> I see now why there aren't checkpoint files being produced. I guess I
> wanted to checkpoint files, in case the EM didn't converge in n steps, then
> I could keep going from that point instead of starting over with >n steps.
>
> Thanks for the response.
>
> Yonatan
>
> On Fri, Jul 7, 2017 at 8:14 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 7/7/17 8:00 PM, Yonatan Zelnik wrote:
> >
> >> Hello,
> >>
> >> I am running an energy minimization script that works quite well, except
> >> that I can't find any of the checkpoint files that mdrun is supposed to
> >> provide. I've been looking through the docs for a while, and I can't
> seem
> >> to find a reason. I have tried the script on multiple systems, and
> >> multiple
> >> installations of gromacs (I am using 5.1.4 with MPI).
> >>
> >> Here is the mdrun command I am using:
> >>
> >> mdrun_sp -v -s em.tpr -o mintraj -g mdlog -c solvated.gro -x
> solvated_traj
> >> -cpo state.cpt -cpt 1.
> >>
> >> The -cpt 1 should give mean that a .cpt file is recorded every minute,
> but
> >> no file is found in the directory where I run the script from. mdrun
> works
> >> well otherwise.
> >>
> >> I'd appreciate any help.
> >>
> >>
> > Energy minimization doesn't produce checkpoint files.  There's no point -
> > there are no velocities or state variables to save.
> >
> > -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
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> > * Please search the archive at http://www.gromacs.org/Support
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>
>
>
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Re: [gmx-users] Regarding creating topology for molecule

[Mark Abraham]

Hi,

The rdf should be constructed from specially constructed index groups, eg
from all N in a specified molecule. Don't try to involve pdb2gmx, it needs
to match the names to the rtp files.

Mark

On Mon, 10 Jul 2017 12:06 Dilip H N  wrote:

> Hello,
> 1] I want to simulate A and B mixtures...but the problem is tht in both the
> say atoms of nitrogen's of both A and B molecules are labelled as N
> onlywhich during the indexing for RDF creates problems...
>
> So in the CHARMM FF .rtp file, i changed the nitrogen (of B molecule) N
> into N1 and thn saved it, and thn did the changes in atom type from N to N1
> in  .pdb/gro file (of B molecule), since now both the nitrogen is labelled
> different in B molecule, and hence now the nitrogen's are labelled
> differently in A and B molecules.
> thn i ran the command as :-
>   gmx pdb2gmx -f a.pdb -o a.gro
>
> but still i am getting the error as:-
> Atom N1 in residue XXX 2 was not found in rtp entry XXX with x atoms
> while sorting atoms.
>
> Why is this error coming inspite of changing the atom type from N to N1
> (ie.,redefined the atoms and checked there is no mismatch between them) in
> the .rtp file, Or still should i do any changes in any other files..??
>  but still i am getting this error... how to solve this error..??
>
> 2] In general, if the atoms are labelled in same type/name for different
> molecules in the .rtp files/any other files, thn how can i correct it and
> get a correct topology file, and get the index's correctly of the atoms
> named same in different molecules, without getting overlapped..??
>
>
> Thank you...
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
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Re: [gmx-users] Invalid order for directive X

[Mark Abraham]

Hi,

The atomtypes directive must appear early. So the acpype files must be
edited to have all the atom types in a block before any of the
moleculetypes. This is covered specifically at
http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx


Mark



On Mon, 10 Jul 2017 13:35 Khadija Amine  wrote:

> Hello,
>
> I have read the documentation and tried to solve the problem but still
> having the same error.
>
> Any suggestions, please?
>
>
> *Khadija Amine*
> Ph.D. Biology and Health
> Biochemistry & Bioinformatics
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[gmx-users] Invalid order for directive X

[Khadija Amine]

Hello,

I have read the documentation and tried to solve the problem but still
having the same error.

Any suggestions, please?


*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
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Re: [gmx-users] Invalid order for directive X

[Nikhil Maroli]

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx
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[gmx-users] Invalid order for directive X

[Khadija Amine]

Dear gromacs users,

I have a protein with two bound ligands, GNP and ACT.

For the protein I have prepared topology with amber ff96. pdb2gmx
created three itp files for the two protein chains and one for CA and
MG ions.


 Fore GNP and ACY I have generated itp files perfectly using acpype
.When I have run gompp program for neutralisation step, I had this
folowing error:

*Syntax error - File ACT.itp, line 3*

*Last line read:*

*'[ atomtypes ]'*

*Invalid order for directive atomtypes It contains an [ atomtypes ]
section defining the GAFF atom types.*



This was my complex topology file:


; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"

#include "ACT.itp"

#include "GNP.itp"

; Include chain topologies
#include "topolo_Protein_chain_A.itp"
#include "topolo_Protein_chain_B.itp"
#include "topolo_Ion_chain_A2.itp"


; Include water topology
#include "amber99sb.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "amber99sb.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
Ion_chain_A21
GNP 1
ACT 1
SOL 20542


And this was my *ACT.itp* file:
; ACT_GMX.itp created by acpype (Rev: 10101) on Mon Jul 10 09:48:02 2017

[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon
Amb
 cc   0.0  0.0   A 3.39967e-01   3.59824e-01 ;
1.91  0.0860
 oo   0.0  0.0   A 2.95992e-01   8.78640e-01 ;
1.66  0.2100
 oh   oh  0.0  0.0   A 3.06647e-01   8.80314e-01 ;
1.72  0.2104
 c3   c3  0.0  0.0   A 3.39967e-01   4.57730e-01 ;
1.91  0.1094
 ho   ho  0.0  0.0   A 0.0e+00   0.0e+00 ;
0.00  0.
 hc   hc  0.0  0.0   A 2.64953e-01   6.56888e-02 ;
1.49  0.0157

 [ moleculetype ]
 ;namenrexcl
  ACT  3

 [ atoms ]
 ;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
  1c 1   ACTC11 0.623101 12.01000 ; qtot 0.623
  2o 1   ACTO12-0.485000 16.0 ; qtot 0.138
  3   oh 1   ACTO23-0.584101 16.0 ; qtot -0.446
  4   c3 1   ACTC24-0.200100 12.01000 ; qtot -0.646
  5   ho 1   ACTH15 0.422000  1.00800 ; qtot -0.224
  6   hc 1   ACTH26 0.074700  1.00800 ; qtot -0.149
  7   hc 1   ACTH37 0.074700  1.00800 ; qtot -0.075
  8   hc 1   ACTH48 0.074700  1.00800 ; qtot -0.000

 [ bonds ]
 ;   ai aj funct   r k
  1  2   11.2183e-015.3363e+05 ; C1 - O1
  1  3   11.3513e-013.3480e+05 ; C1 - O2
  1  4   11.5241e-012.6192e+05 ; C1 - C2
  3  5   19.7300e-023.1079e+05 ; O2 - H1
  4  6   11.0969e-012.7665e+05 ; C2 - H2
  4  7   11.0969e-012.7665e+05 ; C2 - H3
  4  8   11.0969e-012.7665e+05 ; C2 - H4

 [ pairs ]
 ;   ai ajfunct
  2  5  1 ; O1 - H1
  2  6  1 ; O1 - H2
  2  7  1 ; O1 - H3
  2  8  1 ; O1 - H4
  3  6  1 ; O2 - H2
  3  7  1 ; O2 - H3
  3  8  1 ; O2 - H4
  4  5  1 ; C2 - H1

 [ angles ]
 ;   ai aj akfunct   theta cth
  1  3  5  11.0655e+024.1740e+02 ; C1 - O2
- H1
  1  4  6  11.0877e+023.9271e+02 ; C1 - C2
- H2
  1  4  7  11.0877e+023.9271e+02 ; C1 - C2
- H3
  1  4  8  11.0877e+023.9271e+02 ; C1 - C2
- H4
  2  1  3  11.2210e+026.3530e+02 ; O1 - C1
- O2
  2  1  4  11.2320e+025.6400e+02 ; O1 - C1
- C2
  3  1  4  11.1273e+025.7237e+02 ; O2 - C1
- C2
  6  4  7  11.0758e+023.2970e+02 ; H2 - C2
- H3
  6  4  8  11.0758e+023.2970e+02 ; H2 - C2
- H4
  7  4  8  11.0758e+023.2970e+02 ; H3 - C2
- H4

 [ dihedrals ] ; propers
 ; for gromacs 4.5 or higher, using funct 9
 ;i  j  k  l   func   phase kd  pn
  2  1  3  5  9 0.00   7.94960   1 ; O1-C1-
   O2-H1
  2  1  3  5  9   180.00   9.62320   2 ; O1-C1-
   O2-H1
  2  1  4  6  9 0.00   0.0   0 ; O1-C1-
   C2-H2
  2  1  4  6  9 0.00   3.34720   1 ; O1-C1-
   C2-H2
  2  1  4  6  9   

Re: [gmx-users] dihedral angles in CNT

[Alex]

x2top does indeed do that with graphene and CNTs. Strictly speaking, the 
remaining 3/4 of the dihedrals are not redundant, so ideally you should 
test the mechanical properties of your CNT. If the constant for the 
dihedral energy term came from a model, which counts all four dihedrals, 
I would at least try multiplying it by four in your ffbonded file.


Alex

On 7/10/2017 2:39 AM, Zuzana Benkova wrote:

Dear GROMACS users,

I have used the x2top to generate a topology file for the zig-zag carbon 
nanotube (6,0). The pbc were applied. I noticed that the number of generated 
dihedral angles is just a quarter of the total number of the dihedral angles in 
the CNT. Actually, there are four dihedrals around each bond in CNT but only 
one is always considered. I just want to be sure if such a reduction is 
correct. On my opinion this reduction does not affect the definition of the 
conformation of the CNT since the remaining 3/4 of dihedrals are redundant but 
is it correct from the viewpoint of dynamics of the system?
I would appreciate any answer.

Greetings

Zuzana

   


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Re: [gmx-users] Regarding creating topology for molecule

[Nikhil Maroli]

Hi,
You can create a separate index file and feed that for your calculations.


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Nikhil Maroli
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[gmx-users] Regarding creating topology for molecule

[Dilip H N]

Hello,
1] I want to simulate A and B mixtures...but the problem is tht in both the
say atoms of nitrogen's of both A and B molecules are labelled as N
onlywhich during the indexing for RDF creates problems...

So in the CHARMM FF .rtp file, i changed the nitrogen (of B molecule) N
into N1 and thn saved it, and thn did the changes in atom type from N to N1
in  .pdb/gro file (of B molecule), since now both the nitrogen is labelled
different in B molecule, and hence now the nitrogen's are labelled
differently in A and B molecules.
thn i ran the command as :-
  gmx pdb2gmx -f a.pdb -o a.gro

but still i am getting the error as:-
Atom N1 in residue XXX 2 was not found in rtp entry XXX with x atoms
while sorting atoms.

Why is this error coming inspite of changing the atom type from N to N1
(ie.,redefined the atoms and checked there is no mismatch between them) in
the .rtp file, Or still should i do any changes in any other files..??
 but still i am getting this error... how to solve this error..??

2] In general, if the atoms are labelled in same type/name for different
molecules in the .rtp files/any other files, thn how can i correct it and
get a correct topology file, and get the index's correctly of the atoms
named same in different molecules, without getting overlapped..??


Thank you...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

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[gmx-users] dihedral angles in CNT

[Zuzana Benkova]

Dear GROMACS users,

I have used the x2top to generate a topology file for the zig-zag carbon 
nanotube (6,0). The pbc were applied. I noticed that the number of generated 
dihedral angles is just a quarter of the total number of the dihedral angles in 
the CNT. Actually, there are four dihedrals around each bond in CNT but only 
one is always considered. I just want to be sure if such a reduction is 
correct. On my opinion this reduction does not affect the definition of the 
conformation of the CNT since the remaining 3/4 of dihedrals are redundant but 
is it correct from the viewpoint of dynamics of the system? 
I would appreciate any answer.

Greetings

Zuzana 

  
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Re: [gmx-users] Generating GROMACS input file from the GAMESS output file

[조영래]

Thank you Justin
Every time your comment helped me.

I should compare two system that are Zn_binding protein and Fe_binding
protein.

So I need force field that satisfies the following conditions.
First, force field contains two metal ion (Fe and Zn)information.
Second, force field contain metal ion binding mode amino acid information
for example cysteine (CYM) in AMBER.

However many force fields did not satisfied above conditions.
So I would like to generate *.gro *itp file for metal atoms by GAMESS.
But according to your comment this is not correct.

In my case, the metal ions (Fe and Zn) binds one cysteine and two
histidines.
I want to simulate these complexes (i.e. Fe_protein and Zn_protein complex).
Please suggest me an ideal force field that in able to be used for
sumulation of the avode mentaioned complexes.

Thank you a lot
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