[gmx-users] About Free energy surface .....g_sas

[rama david]

Dear Friends,
  I simulated the 4 peptide in water box .
As they come close to each other they start to from anti-parallel
beta sheet structure.



Now I want to draw the Free energy surface for the
same ..How is  there pot energy ???

Would you please tell me how to do it ..

( I read about g_sham -h, I tried it, but not understand properly)

I will be very grateful for your suggestion and help..




With Best Wishes,
Rama David
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[gmx-users] REMD temperature spacing formula

[Nikunj Maheshwari]

Dear all,

We are stuck at the last stage of running a successful REMD.
We have obtained average potential energy by fitting the energy values from
initial MD.
We want to get the temperature spacing for 72 replicas, starting from 280K.
We have gone through numerous papers, but none of them explain clearly how
they got the spacing values.
Is there any equation/formula/web utility which gives the spacing?

Any help will be highly appreciated.

Thank you.
Nikunj & Suhani
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Re:[gmx-users] Applying periodic boundary conditions in energy minimization

[song.yongshun]

Hi,
Actually you have already applied pbc,and there seems nothing wrong.
Some atoms are out of the box is common.
If your box vector is correct,then Gromacs will run successfuly afterwards.
At 2013-04-03 22:51:54,"Abhinav Agrawal"  wrote:
>Hi,
>
>I have a polymer box on which I wish to apply energy minimization. However,
>when I do energy minimization runs to polymer chain unravels and goes out
>of the box. I guess this is because periodic conditions are not applied.
>
>My em.mdp file is:
>
>>
>> ;
>> cpp =  /usr/bin/cpp
>> define  =  -DFLEX_SPC
>> constraints =  none
>> integrator  =  steep
>> nsteps  =  1000
>> ;   Energy minimizing stuff
>> ;
>> emtol   =  2000
>> emstep  =  0.01
>> nstcomm =  1
>> ns_type =  grid
>> rlist   =  1
>> rcoulomb=  1
>> rvdw=  1
>> Tcoupl  =  no
>> Pcoupl  =  no
>> gen_vel =  no
>> pbc  = xyz
>
>
>
>I used the following commands:
>
>grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 2
>>
>
>
>>  mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log
>
>
>
>Can you please tell me what I am doing wrong. Thanks in advance
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[gmx-users] installating GROMACS on windows 7 64 bit system

[imsharmanitin]

i followed the following steps to install gromacs : 

1. Download cygwin from http://www.cygwin.com/ .Installed packages including
"gdb", "make" and "tcsh" 
NOTE : i was not able to find package "gdn" 

2. Downloaded GROMACS (gromacs-4.0.7) source code. 

3. Downloaded fftw-3.2.1.tar.gz 

4. Extracted to C:\fftw-3.2.1 

5. start cygwin and change the directory to your FFTW folder: cd
c:\fftw-3.2.1 

6. ./configure --enable-threads --enable-sse --enable-float 

7. make 

8. make install 

9. make distclean 

10. Extracted gromacs to C:\gromacs-4.0.7 and in the cygwin console, changed
directory to the gromacs folder: cd C:\gromacs-4.0.7 

11.  ./configure --enable-shared LDFLAGS='-L/usr/local/lib' 

12.  make 

13. make install 

14. make links 

15. make clean 

16. i downloaded the test set gmxtest-4.0.4 and extracted it to C:\gmxtest 

17. in the cygwin console, changed directory to the gmxtest folder: cd
C:\gmxtest 

18. source /usr/local/gromacs/bin/GMXRC 

19. ./gmxtest.pl all 

Got the following result 

"$ ./gmxtest.pl all 
All 16 simple tests PASSED 
FAILED. Check files in aminoacids 
FAILED. Check files in field 
FAILED. Check files in tip4p 
FAILED. Check files in water 
4 out of 14 complex tests FAILED 
FAILED. Check files in kernel020 
FAILED. Check files in kernel120 
FAILED. Check files in kernel121 
FAILED. Check files in kernel122 
FAILED. Check files in kernel123 
FAILED. Check files in kernel124 
FAILED. Check files in kernel220 
FAILED. Check files in kernel221 
FAILED. Check files in kernel222 
FAILED. Check files in kernel223 
FAILED. Check files in kernel224 
FAILED. Check files in kernel320 
FAILED. Check files in kernel321 
FAILED. Check files in kernel322 
FAILED. Check files in kernel323 
FAILED. Check files in kernel324 
16 out of 63 kernel tests FAILED 
N  Reference   This test 
  10-33.9883-29.5518 
  11-33.9883-29.5518 
There were 2 differences in final energy with the reference file 
All 45 pdb2gmx tests PASSED 
pdb2gmx tests FAILED " 

what is the error and how can i eliminate it ?




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Re: [gmx-users] Simulation of the HEM-containing proteins

[James Starlight]

It was strange for me the big number of such errors :)
May the construction of new scheme for the hydrogens  in the .hdb file
partly solve my problem ? ( as I've mentioned previously i had mismatch in
2 hydrogens ( in comparison to the NMR-like structure).
Should also HEME be added in the residuetype.dat as the part of the protein?

Finally I'll be thankful to everyone who could provide me with the any
cytochrome properly parametrized in charmm :)

James

2013/4/3 Justin Lemkul 

> On Wed, Apr 3, 2013 at 10:27 AM, James Starlight  >wrote:
>
> > I've successfully parametrize cytochrome-HEME complex by means pdb2gmx
> but
> > after processing that structure to grompp I've obtained errors like
> >
> > ERROR 1 [file topol.top, line 2106]:
> >   No default Bond types
> >
> >
> > ERROR 2 [file topol.top, line 2144]:
> >   No default Bond types
> >
> >
> > ERROR 3 [file topol.top, line 3153]:
> >   No default Bond types
> >
> >
> > ERROR 4 [file topol.top, line 8725]:
> >   No default U-B types
> >
> >
> > ERROR 5 [file topol.top, line 8792]:
> >   No default U-B types
> >
> >
> > ERROR 6 [file topol.top, line 10624]:
> >   No default U-B types
> >
> >
> > ERROR 7 [file topol.top, line 10625]:
> >   No default U-B types
> >
> >
> > ERROR 8 [file topol.top, line 11382]:
> >   No default U-B types
> >
> >
> > ERROR 9 [file topol.top, line 11383]:
> >   No default U-B types
> >
> >
> > ERROR 10 [file topol.top, line 11384]:
> >   No default U-B types
> >
> >
> > ERROR 11 [file topol.top, line 11385]:
> >   No default U-B types
> >
> >
> > ERROR 12 [file topol.top, line 11491]:
> >   No default U-B types
> >
> >
> > ERROR 13 [file topol.top, line 11492]:
> >   No default U-B types
> >
> >
> > ERROR 14 [file topol.top, line 11493]:
> >   No default U-B types
> >
> >
> > ERROR 15 [file topol.top, line 11506]:
> >   No default U-B types
> >
> >
> > ERROR 16 [file topol.top, line 11507]:
> >   No default U-B types
> >
> >
> > ERROR 17 [file topol.top, line 11508]:
> >   No default U-B types
> >
> >
> > ERROR 18 [file topol.top, line 12147]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 19 [file topol.top, line 12148]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 20 [file topol.top, line 12149]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 21 [file topol.top, line 12150]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 22 [file topol.top, line 12151]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 23 [file topol.top, line 12152]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 24 [file topol.top, line 12247]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 25 [file topol.top, line 12248]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 26 [file topol.top, line 12249]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 27 [file topol.top, line 12250]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 28 [file topol.top, line 12251]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 29 [file topol.top, line 12252]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 30 [file topol.top, line 14948]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 31 [file topol.top, line 14950]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 32 [file topol.top, line 14952]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 33 [file topol.top, line 14956]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 34 [file topol.top, line 14957]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 35 [file topol.top, line 14958]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 36 [file topol.top, line 14959]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 37 [file topol.top, line 14960]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 38 [file topol.top, line 14961]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 39 [file topol.top, line 14962]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 40 [file topol.top, line 14963]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 41 [file topol.top, line 14964]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 42 [file topol.top, line 14965]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 43 [file topol.top, line 14966]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 44 [file topol.top, line 16263]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 45 [file topol.top, line 16264]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 46 [file topol.top, line 16269]:
> >   No default Proper Dih. types
> >
> >
> > ERROR 47 [file topol.top, line 16270]:
> >   No default Proper Dih. types
> >
> > Excluding 3 bonded neighbours molecule type 'Protein'
> > Excluding 2 bonded neighbours molecule type 'SOL'
> >
> > NOTE 3 [file topol.top, line 16745]:
> >   System has non-zero total charge: 7.01
> >   Total charge should normally be an integer. See
> >   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> >   for discussion on how close it should be to an integer.
> >
> >
> > -

Re: [gmx-users] Salt bridge observation

[Kavyashree M]

Sir,

That is true, previously you had explained regarding this.

Calculation using g_saltbr
1. For g_saltbr I included the following residues -
ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated
which contained only these residues. sb was calculated using -

   g_saltbr -f traj.xtc  -s md.tpr  -b 4000 -e 4000 -t 0.4 -sep

2. Files that were generated were filtered and only those having
sb between ASP, GLU and ARG LYS were retained.

3. Further, out of these sbs, those which had the following atoms
CG  ASP, CD  GLU, NE  ARG, NH1 ARG, NH2 ARG, NZ  LYS
were retained.

Calculation using g_hbond -
It was done using the index file mentioned in my previous post using

g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm
-hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000

So essentially the final results in both are composed of sbs formed
between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr
while charged atoms in case of g_hbond.

The comparison showed that all sbs from g_hbond were present
in the output from g_saltbr. But g_saltbr had some additional sbs
off-course between the same charged groups. But only the distance
was greater than 4 Ang for ex-
distance between NH2 ARG and OD2 ASP is 4.32Ang
Since it considers charged group CG of ASP instead of OD2 ASP
distance between NH2 ARG and CG ASP is 5.54 Ang

There are some 10 more such examples. I can send the calculations
if requires.

Thank you
Regards
Kavya





On Wed, Apr 3, 2013 at 10:25 PM, Justin Lemkul  wrote:

> On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M  wrote:
>
> > Dear users,
> >
> > This is regarding an observation while calculating the
> > salt bridge (sb) using g_saltbr.
> >
> >
> > I used g_saltbr and g_hbond (with contact option) with
> > a cut of of 4Ang, for calculating sb in the whole protein
> > at a single frame.
> >
> > I made sure that I considered sb between same set of
> > residues (ASP, GLU with LYS ARG) in both calculations.
> > and filtered accordingly.
> >
> > While checking the individual sb it was found that most
> > of the results from g_saltbr matches with g_hbond but
> > g_saltbr gives some extra sbs. On checking these extra
> > sb it was found that the distance between the atoms
> > forming sb are more than the cut of I had mentioned (4 Ang).
> >
> > Not sure why it is like this. But just wanted to convey this
> > observation.
> >
> >
> Please provide a concrete example.  Note that running g_saltbr and g_hbond
> (with the index files mentioned before) should not be expected to produce
> equivalent result.  g_saltbr is relatively stupid; it considers any group
> with a charge ± 0.2 to be capable of participating in a salt bridge.  In
> some cases, this will include methylene groups or others than are near the
> actual charged groups.  Such behavior could easily account for whatever
> observation you're making.
>
> -Justin
>
> --
>
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] Re: cannot read frames out from trr files

[mu xiaojia]

Thanks Justin,

It never happens to my simulations before, is there anyway to figure out
what caused this corruption?  the log file and screen outputs didn't
mentioned any error message. I am wandering if it was caused by the
unstable super-cluster I am currently using, because on another
super-clusters, it never happened before.


On Wed, Apr 3, 2013 at 7:45 PM, Justin Lemkul  wrote:

>
>
> On 4/3/13 8:42 PM, mu xiaojia wrote:
>
>> Sorry for the typo, the last evidence"4) I also compared the generated
>> files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching
>> 100ns, the size would **NOT*** be the same as A."
>>
>>
> You probably have a corrupted frame.  The simulation continued and the
> .trr file continued being written, so you see comparable file sizes.
>
> -Justin
>
>
>> On Wed, Apr 3, 2013 at 7:25 PM, mu xiaojia 
>> wrote:
>>
>>  Dear GMX users,
>>>
>>> I am not sure if someone has similar problems before. I cannot read half
>>> of the frames from trr file after md simulation, and I believe my
>>> simulation has already completed.
>>>
>>> I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the
>>> only difference between A and B is they are npt simulations under
>>> different
>>> temperature (in mdp file, "ref_t" part )and such difference would not
>>> cause
>>> crash of the simulation. I have successfully finished A, everything looks
>>> perfect (frames can be successfully extracted), but for B, I could not
>>> extract last 70ns' frames from trr.
>>>
>>> 1) My command is like: mdrun_mpi -s -deffnm MD_A -cpi -append, because I
>>> am using super computer so the job will be restarted for multiple times.
>>>
>>> 2) both simulation are 100ns, both log files indicate that they have
>>> finished 100ns simulations. I checked my screen out put for B, whenever
>>> it
>>> restarted, the output on screen is correct and continuously ( something
>>> like: 1 steps, 10.0 ps (continuing from step 95963500,
>>>  95963.5
>>> ps).
>>>
>>> 3) With gmxcheck, it looks that my B simulation only reached 29,7ns(which
>>> means only the first two restart simulation were recorded into trr, which
>>> log files are not saying in this way.)
>>> *
>>> *
>>> *For system A (the successful one), it shows*
>>>
>>> Reading frame   0 time0.000
>>> # Atoms  72166
>>> Last frame 2000 time 10.000
>>>
>>>
>>> Item#frames Timestep (ps)
>>> Step   200150
>>> Time   200150
>>> Lambda   200150
>>> Coords 200150
>>> Velocities 200150
>>> Forces   0
>>> Box200150
>>>
>>> *for system B (the failed one)*
>>>
>>> Reading frame   0 time0.000
>>> # Atoms  72166
>>> Reading frame 500 time 25000.000
>>>
>>>
>>> Item#frames Timestep (ps)
>>> Step   59650
>>> Time   59650
>>> Lambda 59650
>>> Coords 59650
>>> Velocities 59650
>>> Forces   0
>>> Box59650
>>>
>>> 4) I also compared the generated files' sizes, A = B in trr, edr , gro,
>>> cpt, if B crashes before reaching 100ns, the size would be the same as A.
>>>
>>> I am wondering what was wrong with my trr file of B . I appreciate for
>>> any
>>> suggestions!
>>>
>>> Sincerely
>>>
>>> Xiaojia
>>>
>>>
>>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
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[gmx-users] surface tension

[Elisabeth]

Hello all,

Does anyone know how one can study the effect of pressure on surface
tension of pure liquids?

Thanks,
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[gmx-users] Re: Applying periodic boundary conditions in energy minimization

[Abhinav Agrawal]

> > Hi,
> >
> > I have a polymer box on which I wish to apply energy minimization.
> However,
> > when I do energy minimization runs to polymer chain unravels and goes out
> > of the box. I guess this is because periodic conditions are not applied.
> >
> > My em.mdp file is:
> >
> > >
> > > ;
> > > cpp =  /usr/bin/cpp
> > > define  =  -DFLEX_SPC
> > > constraints =  none
> > > integrator  =  steep
> > > nsteps  =  1000
> > > ;   Energy minimizing stuff
> > > ;
> > > emtol   =  2000
> > > emstep  =  0.01
> > > nstcomm =  1
> > > ns_type =  grid
> > > rlist   =  1
> > > rcoulomb=  1
> > > rvdw=  1
> > > Tcoupl  =  no
> > > Pcoupl  =  no
> > > gen_vel =  no
> > > pbc  = xyz
> >
> >
> This last line means PBC are being applied. Your observations are
> consistent with using a box that is too small for the solute, but since you
> haven't supplied information as to (1) what the system is, (2) how you
> built it, or (3) how large the box is, there's very little to say beyond
> speculation.
>
> -Justin
>
> --
>
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>

I am using a composite system of polymer and clay. The composite box (5.8
nm * 5.8 nm *7 nm) is made from combining a polymer box (5.7 nm * 5.7 nm *
5.7 nm) and clay box (5.5 nm * 5.1 nm * 1 nm) using editconf and genbox.

Should I increase the size of the composite box. Also, If I increase the
size of the box how do I ensure that the density of the system does not
chance. Thanks for your help.
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Re: [gmx-users] Re: cannot read frames out from trr files

[Justin Lemkul]

On 4/3/13 8:42 PM, mu xiaojia wrote:

Sorry for the typo, the last evidence"4) I also compared the generated
files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching
100ns, the size would **NOT*** be the same as A."



You probably have a corrupted frame.  The simulation continued and the .trr file 
continued being written, so you see comparable file sizes.


-Justin



On Wed, Apr 3, 2013 at 7:25 PM, mu xiaojia  wrote:


Dear GMX users,

I am not sure if someone has similar problems before. I cannot read half
of the frames from trr file after md simulation, and I believe my
simulation has already completed.

I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the
only difference between A and B is they are npt simulations under different
temperature (in mdp file, "ref_t" part )and such difference would not cause
crash of the simulation. I have successfully finished A, everything looks
perfect (frames can be successfully extracted), but for B, I could not
extract last 70ns' frames from trr.

1) My command is like: mdrun_mpi -s -deffnm MD_A -cpi -append, because I
am using super computer so the job will be restarted for multiple times.

2) both simulation are 100ns, both log files indicate that they have
finished 100ns simulations. I checked my screen out put for B, whenever it
restarted, the output on screen is correct and continuously ( something
like: 1 steps, 10.0 ps (continuing from step 95963500,  95963.5
ps).

3) With gmxcheck, it looks that my B simulation only reached 29,7ns(which
means only the first two restart simulation were recorded into trr, which
log files are not saying in this way.)
*
*
*For system A (the successful one), it shows*
Reading frame   0 time0.000
# Atoms  72166
Last frame 2000 time 10.000


Item#frames Timestep (ps)
Step   200150
Time   200150
Lambda   200150
Coords 200150
Velocities 200150
Forces   0
Box200150

*for system B (the failed one)*
Reading frame   0 time0.000
# Atoms  72166
Reading frame 500 time 25000.000


Item#frames Timestep (ps)
Step   59650
Time   59650
Lambda 59650
Coords 59650
Velocities 59650
Forces   0
Box59650

4) I also compared the generated files' sizes, A = B in trr, edr , gro,
cpt, if B crashes before reaching 100ns, the size would be the same as A.

I am wondering what was wrong with my trr file of B . I appreciate for any
suggestions!

Sincerely

Xiaojia




--


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


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[gmx-users] Re: cannot read frames out from trr files

[mu xiaojia]

Sorry for the typo, the last evidence"4) I also compared the generated
files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching
100ns, the size would **NOT*** be the same as A."


On Wed, Apr 3, 2013 at 7:25 PM, mu xiaojia  wrote:

> Dear GMX users,
>
> I am not sure if someone has similar problems before. I cannot read half
> of the frames from trr file after md simulation, and I believe my
> simulation has already completed.
>
> I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the
> only difference between A and B is they are npt simulations under different
> temperature (in mdp file, "ref_t" part )and such difference would not cause
> crash of the simulation. I have successfully finished A, everything looks
> perfect (frames can be successfully extracted), but for B, I could not
> extract last 70ns' frames from trr.
>
> 1) My command is like: mdrun_mpi -s -deffnm MD_A -cpi -append, because I
> am using super computer so the job will be restarted for multiple times.
>
> 2) both simulation are 100ns, both log files indicate that they have
> finished 100ns simulations. I checked my screen out put for B, whenever it
> restarted, the output on screen is correct and continuously ( something
> like: 1 steps, 10.0 ps (continuing from step 95963500,  95963.5
> ps).
>
> 3) With gmxcheck, it looks that my B simulation only reached 29,7ns(which
> means only the first two restart simulation were recorded into trr, which
> log files are not saying in this way.)
> *
> *
> *For system A (the successful one), it shows*
> Reading frame   0 time0.000
> # Atoms  72166
> Last frame 2000 time 10.000
>
>
> Item#frames Timestep (ps)
> Step   200150
> Time   200150
> Lambda   200150
> Coords 200150
> Velocities 200150
> Forces   0
> Box200150
>
> *for system B (the failed one)*
> Reading frame   0 time0.000
> # Atoms  72166
> Reading frame 500 time 25000.000
>
>
> Item#frames Timestep (ps)
> Step   59650
> Time   59650
> Lambda 59650
> Coords 59650
> Velocities 59650
> Forces   0
> Box59650
>
> 4) I also compared the generated files' sizes, A = B in trr, edr , gro,
> cpt, if B crashes before reaching 100ns, the size would be the same as A.
>
> I am wondering what was wrong with my trr file of B . I appreciate for any
> suggestions!
>
> Sincerely
>
> Xiaojia
>
>
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[gmx-users] cannot read frames out from trr files

[mu xiaojia]

Dear GMX users,

I am not sure if someone has similar problems before. I cannot read half of
the frames from trr file after md simulation, and I believe my simulation
has already completed.

I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the
only difference between A and B is they are npt simulations under different
temperature (in mdp file, "ref_t" part )and such difference would not cause
crash of the simulation. I have successfully finished A, everything looks
perfect (frames can be successfully extracted), but for B, I could not
extract last 70ns' frames from trr.

1) My command is like: mdrun_mpi -s -deffnm MD_A -cpi -append, because I am
using super computer so the job will be restarted for multiple times.

2) both simulation are 100ns, both log files indicate that they have
finished 100ns simulations. I checked my screen out put for B, whenever it
restarted, the output on screen is correct and continuously ( something
like: 1 steps, 10.0 ps (continuing from step 95963500,  95963.5
ps).

3) With gmxcheck, it looks that my B simulation only reached 29,7ns(which
means only the first two restart simulation were recorded into trr, which
log files are not saying in this way.)
*
*
*For system A (the successful one), it shows*
Reading frame   0 time0.000
# Atoms  72166
Last frame 2000 time 10.000


Item#frames Timestep (ps)
Step   200150
Time   200150
Lambda   200150
Coords 200150
Velocities 200150
Forces   0
Box200150

*for system B (the failed one)*
Reading frame   0 time0.000
# Atoms  72166
Reading frame 500 time 25000.000


Item#frames Timestep (ps)
Step   59650
Time   59650
Lambda 59650
Coords 59650
Velocities 59650
Forces   0
Box59650

4) I also compared the generated files' sizes, A = B in trr, edr , gro,
cpt, if B crashes before reaching 100ns, the size would be the same as A.

I am wondering what was wrong with my trr file of B . I appreciate for any
suggestions!

Sincerely

Xiaojia
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Re: [gmx-users] g_dipoles: "index group is not a set of the whole molecules"

[Justin Lemkul]

On 4/3/13 11:13 AM, Oleksandr Sushko wrote:

Dear Gromacs users,
can you help me please with next issue:
I'm analysing solvation shell of water molecules around a protein.
I use g_select to select different layers of water based on distance criteria.
The output index file contains all the atoms which satisfy the specified 
criteria.
For some molecules on the edge only some atoms are within the specified distance
from protein.
So some molecules in the selection are represented only by 1 or 2 atoms out of 
3.

Such selection works fine for example for g_hbond, but it does not work for
g_dipoles.
The error in case of g_dipoles is: "index group is not a set of whole molecules"

is there a smart way (except manual editing of .ndx file) to select the whole
molecules within some distance from protein (with COM within specified distance
from protein surface)?



It would help to know exactly what your selection syntax was.  I think you can 
use something like "same residue as (within ...)" for your selection, but I 
haven't tried it.


-Justin

--


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


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[gmx-users] New python package with gromacs support

[Gabriele Lanaro]

Hello GMX users, I just wanted to share a python library I made that may be
of help to someone. It includes a molecular viewer and native parsing of
xtc and edr files.

Go check it out! http://chemlab.github.com/chemlab

Thank you
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Re: [gmx-users] Salt bridge observation

[Justin Lemkul]

On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M  wrote:

> Dear users,
>
> This is regarding an observation while calculating the
> salt bridge (sb) using g_saltbr.
>
>
> I used g_saltbr and g_hbond (with contact option) with
> a cut of of 4Ang, for calculating sb in the whole protein
> at a single frame.
>
> I made sure that I considered sb between same set of
> residues (ASP, GLU with LYS ARG) in both calculations.
> and filtered accordingly.
>
> While checking the individual sb it was found that most
> of the results from g_saltbr matches with g_hbond but
> g_saltbr gives some extra sbs. On checking these extra
> sb it was found that the distance between the atoms
> forming sb are more than the cut of I had mentioned (4 Ang).
>
> Not sure why it is like this. But just wanted to convey this
> observation.
>
>
Please provide a concrete example.  Note that running g_saltbr and g_hbond
(with the index files mentioned before) should not be expected to produce
equivalent result.  g_saltbr is relatively stupid; it considers any group
with a charge ± 0.2 to be capable of participating in a salt bridge.  In
some cases, this will include methylene groups or others than are near the
actual charged groups.  Such behavior could easily account for whatever
observation you're making.

-Justin

-- 



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


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[gmx-users] Salt bridge observation

[Kavyashree M]

Dear users,

This is regarding an observation while calculating the
salt bridge (sb) using g_saltbr.


I used g_saltbr and g_hbond (with contact option) with
a cut of of 4Ang, for calculating sb in the whole protein
at a single frame.

I made sure that I considered sb between same set of
residues (ASP, GLU with LYS ARG) in both calculations.
and filtered accordingly.

While checking the individual sb it was found that most
of the results from g_saltbr matches with g_hbond but
g_saltbr gives some extra sbs. On checking these extra
sb it was found that the distance between the atoms
forming sb are more than the cut of I had mentioned (4 Ang).

Not sure why it is like this. But just wanted to convey this
observation.

Thank you
regards
Kavya
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Re: [gmx-users] Applying periodic boundary conditions in energy minimization

[Tsjerk Wassenaar]

There is no outside of the box.

Tsjerk


On Wed, Apr 3, 2013 at 4:51 PM, Abhinav Agrawal  wrote:

> Hi,
>
> I have a polymer box on which I wish to apply energy minimization. However,
> when I do energy minimization runs to polymer chain unravels and goes out
> of the box. I guess this is because periodic conditions are not applied.
>
> My em.mdp file is:
>
> >
> > ;
> > cpp =  /usr/bin/cpp
> > define  =  -DFLEX_SPC
> > constraints =  none
> > integrator  =  steep
> > nsteps  =  1000
> > ;   Energy minimizing stuff
> > ;
> > emtol   =  2000
> > emstep  =  0.01
> > nstcomm =  1
> > ns_type =  grid
> > rlist   =  1
> > rcoulomb=  1
> > rvdw=  1
> > Tcoupl  =  no
> > Pcoupl  =  no
> > gen_vel =  no
> > pbc  = xyz
>
>
>
> I used the following commands:
>
> grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 2
> >
>
>
> >  mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log
>
>
>
> Can you please tell me what I am doing wrong. Thanks in advance
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] g_dipoles: "index group is not a set of the whole molecules"

[Oleksandr Sushko]

Dear Gromacs users,
can you help me please with next issue:
I'm analysing solvation shell of water molecules around a protein.
I use g_select to select different layers of water based on distance 
criteria.
The output index file contains all the atoms which satisfy the specified 
criteria.
For some molecules on the edge only some atoms are within the specified 
distance from protein.
So some molecules in the selection are represented only by 1 or 2 atoms 
out of 3.


Such selection works fine for example for g_hbond, but it does not work 
for g_dipoles.
The error in case of g_dipoles is: "index group is not a set of whole 
molecules"


is there a smart way (except manual editing of .ndx file) to select the 
whole molecules within some distance from protein (with COM within 
specified distance from protein surface)?


thanks,
Oleksandr


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Re: [gmx-users] Applying periodic boundary conditions in energy minimization

[Justin Lemkul]

On Wed, Apr 3, 2013 at 10:51 AM, Abhinav Agrawal wrote:

> Hi,
>
> I have a polymer box on which I wish to apply energy minimization. However,
> when I do energy minimization runs to polymer chain unravels and goes out
> of the box. I guess this is because periodic conditions are not applied.
>
> My em.mdp file is:
>
> >
> > ;
> > cpp =  /usr/bin/cpp
> > define  =  -DFLEX_SPC
> > constraints =  none
> > integrator  =  steep
> > nsteps  =  1000
> > ;   Energy minimizing stuff
> > ;
> > emtol   =  2000
> > emstep  =  0.01
> > nstcomm =  1
> > ns_type =  grid
> > rlist   =  1
> > rcoulomb=  1
> > rvdw=  1
> > Tcoupl  =  no
> > Pcoupl  =  no
> > gen_vel =  no
> > pbc  = xyz
>
>
This last line means PBC are being applied. Your observations are
consistent with using a box that is too small for the solute, but since you
haven't supplied information as to (1) what the system is, (2) how you
built it, or (3) how large the box is, there's very little to say beyond
speculation.

-Justin

-- 



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


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Re: [gmx-users] Using two integrators in energy minimization

[Justin Lemkul]

On Wed, Apr 3, 2013 at 11:07 AM, Abhinav Agrawal wrote:

> I want to use both steepest descent and conjugate gradient in my energy
> minimization. I need the system to use steepest descent for a given number
> of steps and then switch over  to conjugate gradient. Can anyone please
> suggest how I can do this? How should I make the em.mdp file
>
>
You make two, one that specifies the steepest descent process, and one that
specifies CG. The output of step 1 becomes the input for step 2.

-Justin

-- 



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


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[gmx-users] Using two integrators in energy minimization

[Abhinav Agrawal]

I want to use both steepest descent and conjugate gradient in my energy
minimization. I need the system to use steepest descent for a given number
of steps and then switch over  to conjugate gradient. Can anyone please
suggest how I can do this? How should I make the em.mdp file

Thanks in advance.
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[gmx-users] Applying periodic boundary conditions in energy minimization

[Abhinav Agrawal]

Hi,

I have a polymer box on which I wish to apply energy minimization. However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess this is because periodic conditions are not applied.

My em.mdp file is:

>
> ;
> cpp =  /usr/bin/cpp
> define  =  -DFLEX_SPC
> constraints =  none
> integrator  =  steep
> nsteps  =  1000
> ;   Energy minimizing stuff
> ;
> emtol   =  2000
> emstep  =  0.01
> nstcomm =  1
> ns_type =  grid
> rlist   =  1
> rcoulomb=  1
> rvdw=  1
> Tcoupl  =  no
> Pcoupl  =  no
> gen_vel =  no
> pbc  = xyz



I used the following commands:

grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 2
>


>  mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log



Can you please tell me what I am doing wrong. Thanks in advance
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Re: [gmx-users] Simulation of the HEM-containing proteins

[Justin Lemkul]

On Wed, Apr 3, 2013 at 10:27 AM, James Starlight wrote:

> I've successfully parametrize cytochrome-HEME complex by means pdb2gmx but
> after processing that structure to grompp I've obtained errors like
>
> ERROR 1 [file topol.top, line 2106]:
>   No default Bond types
>
>
> ERROR 2 [file topol.top, line 2144]:
>   No default Bond types
>
>
> ERROR 3 [file topol.top, line 3153]:
>   No default Bond types
>
>
> ERROR 4 [file topol.top, line 8725]:
>   No default U-B types
>
>
> ERROR 5 [file topol.top, line 8792]:
>   No default U-B types
>
>
> ERROR 6 [file topol.top, line 10624]:
>   No default U-B types
>
>
> ERROR 7 [file topol.top, line 10625]:
>   No default U-B types
>
>
> ERROR 8 [file topol.top, line 11382]:
>   No default U-B types
>
>
> ERROR 9 [file topol.top, line 11383]:
>   No default U-B types
>
>
> ERROR 10 [file topol.top, line 11384]:
>   No default U-B types
>
>
> ERROR 11 [file topol.top, line 11385]:
>   No default U-B types
>
>
> ERROR 12 [file topol.top, line 11491]:
>   No default U-B types
>
>
> ERROR 13 [file topol.top, line 11492]:
>   No default U-B types
>
>
> ERROR 14 [file topol.top, line 11493]:
>   No default U-B types
>
>
> ERROR 15 [file topol.top, line 11506]:
>   No default U-B types
>
>
> ERROR 16 [file topol.top, line 11507]:
>   No default U-B types
>
>
> ERROR 17 [file topol.top, line 11508]:
>   No default U-B types
>
>
> ERROR 18 [file topol.top, line 12147]:
>   No default Proper Dih. types
>
>
> ERROR 19 [file topol.top, line 12148]:
>   No default Proper Dih. types
>
>
> ERROR 20 [file topol.top, line 12149]:
>   No default Proper Dih. types
>
>
> ERROR 21 [file topol.top, line 12150]:
>   No default Proper Dih. types
>
>
> ERROR 22 [file topol.top, line 12151]:
>   No default Proper Dih. types
>
>
> ERROR 23 [file topol.top, line 12152]:
>   No default Proper Dih. types
>
>
> ERROR 24 [file topol.top, line 12247]:
>   No default Proper Dih. types
>
>
> ERROR 25 [file topol.top, line 12248]:
>   No default Proper Dih. types
>
>
> ERROR 26 [file topol.top, line 12249]:
>   No default Proper Dih. types
>
>
> ERROR 27 [file topol.top, line 12250]:
>   No default Proper Dih. types
>
>
> ERROR 28 [file topol.top, line 12251]:
>   No default Proper Dih. types
>
>
> ERROR 29 [file topol.top, line 12252]:
>   No default Proper Dih. types
>
>
> ERROR 30 [file topol.top, line 14948]:
>   No default Proper Dih. types
>
>
> ERROR 31 [file topol.top, line 14950]:
>   No default Proper Dih. types
>
>
> ERROR 32 [file topol.top, line 14952]:
>   No default Proper Dih. types
>
>
> ERROR 33 [file topol.top, line 14956]:
>   No default Proper Dih. types
>
>
> ERROR 34 [file topol.top, line 14957]:
>   No default Proper Dih. types
>
>
> ERROR 35 [file topol.top, line 14958]:
>   No default Proper Dih. types
>
>
> ERROR 36 [file topol.top, line 14959]:
>   No default Proper Dih. types
>
>
> ERROR 37 [file topol.top, line 14960]:
>   No default Proper Dih. types
>
>
> ERROR 38 [file topol.top, line 14961]:
>   No default Proper Dih. types
>
>
> ERROR 39 [file topol.top, line 14962]:
>   No default Proper Dih. types
>
>
> ERROR 40 [file topol.top, line 14963]:
>   No default Proper Dih. types
>
>
> ERROR 41 [file topol.top, line 14964]:
>   No default Proper Dih. types
>
>
> ERROR 42 [file topol.top, line 14965]:
>   No default Proper Dih. types
>
>
> ERROR 43 [file topol.top, line 14966]:
>   No default Proper Dih. types
>
>
> ERROR 44 [file topol.top, line 16263]:
>   No default Proper Dih. types
>
>
> ERROR 45 [file topol.top, line 16264]:
>   No default Proper Dih. types
>
>
> ERROR 46 [file topol.top, line 16269]:
>   No default Proper Dih. types
>
>
> ERROR 47 [file topol.top, line 16270]:
>   No default Proper Dih. types
>
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 3 [file topol.top, line 16745]:
>   System has non-zero total charge: 7.01
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer.
>
>
> ---
> Program grompp, VERSION 4.6
> Source code file:
> /home/own/Documents/distr/gromacs-4.6/src/kernel/grompp.c, line: 1593
>
> Fatal error:
> There were 47 errors in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> During visualization of the complex.gro file I didnt observe any
> distortions in the geometry of heme-cytochrome complex (it looks like NMR
> structure) but why that errors occured ?
>
>
Heme is tricky, and this error comes up every time someone tries to use
heme in Gromacs (see the archive for tips and possible solutions).
 Parameters are missing for bonded interactions, so either add them
directly to the .top or to ffbonded.itp.  You'll have to search the
literature for suitable parameters or derive them yourself

Re: [gmx-users] Simulation of the HEM-containing proteins

[James Starlight]

I've successfully parametrize cytochrome-HEME complex by means pdb2gmx but
after processing that structure to grompp I've obtained errors like

ERROR 1 [file topol.top, line 2106]:
  No default Bond types


ERROR 2 [file topol.top, line 2144]:
  No default Bond types


ERROR 3 [file topol.top, line 3153]:
  No default Bond types


ERROR 4 [file topol.top, line 8725]:
  No default U-B types


ERROR 5 [file topol.top, line 8792]:
  No default U-B types


ERROR 6 [file topol.top, line 10624]:
  No default U-B types


ERROR 7 [file topol.top, line 10625]:
  No default U-B types


ERROR 8 [file topol.top, line 11382]:
  No default U-B types


ERROR 9 [file topol.top, line 11383]:
  No default U-B types


ERROR 10 [file topol.top, line 11384]:
  No default U-B types


ERROR 11 [file topol.top, line 11385]:
  No default U-B types


ERROR 12 [file topol.top, line 11491]:
  No default U-B types


ERROR 13 [file topol.top, line 11492]:
  No default U-B types


ERROR 14 [file topol.top, line 11493]:
  No default U-B types


ERROR 15 [file topol.top, line 11506]:
  No default U-B types


ERROR 16 [file topol.top, line 11507]:
  No default U-B types


ERROR 17 [file topol.top, line 11508]:
  No default U-B types


ERROR 18 [file topol.top, line 12147]:
  No default Proper Dih. types


ERROR 19 [file topol.top, line 12148]:
  No default Proper Dih. types


ERROR 20 [file topol.top, line 12149]:
  No default Proper Dih. types


ERROR 21 [file topol.top, line 12150]:
  No default Proper Dih. types


ERROR 22 [file topol.top, line 12151]:
  No default Proper Dih. types


ERROR 23 [file topol.top, line 12152]:
  No default Proper Dih. types


ERROR 24 [file topol.top, line 12247]:
  No default Proper Dih. types


ERROR 25 [file topol.top, line 12248]:
  No default Proper Dih. types


ERROR 26 [file topol.top, line 12249]:
  No default Proper Dih. types


ERROR 27 [file topol.top, line 12250]:
  No default Proper Dih. types


ERROR 28 [file topol.top, line 12251]:
  No default Proper Dih. types


ERROR 29 [file topol.top, line 12252]:
  No default Proper Dih. types


ERROR 30 [file topol.top, line 14948]:
  No default Proper Dih. types


ERROR 31 [file topol.top, line 14950]:
  No default Proper Dih. types


ERROR 32 [file topol.top, line 14952]:
  No default Proper Dih. types


ERROR 33 [file topol.top, line 14956]:
  No default Proper Dih. types


ERROR 34 [file topol.top, line 14957]:
  No default Proper Dih. types


ERROR 35 [file topol.top, line 14958]:
  No default Proper Dih. types


ERROR 36 [file topol.top, line 14959]:
  No default Proper Dih. types


ERROR 37 [file topol.top, line 14960]:
  No default Proper Dih. types


ERROR 38 [file topol.top, line 14961]:
  No default Proper Dih. types


ERROR 39 [file topol.top, line 14962]:
  No default Proper Dih. types


ERROR 40 [file topol.top, line 14963]:
  No default Proper Dih. types


ERROR 41 [file topol.top, line 14964]:
  No default Proper Dih. types


ERROR 42 [file topol.top, line 14965]:
  No default Proper Dih. types


ERROR 43 [file topol.top, line 14966]:
  No default Proper Dih. types


ERROR 44 [file topol.top, line 16263]:
  No default Proper Dih. types


ERROR 45 [file topol.top, line 16264]:
  No default Proper Dih. types


ERROR 46 [file topol.top, line 16269]:
  No default Proper Dih. types


ERROR 47 [file topol.top, line 16270]:
  No default Proper Dih. types

Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 3 [file topol.top, line 16745]:
  System has non-zero total charge: 7.01
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.


---
Program grompp, VERSION 4.6
Source code file:
/home/own/Documents/distr/gromacs-4.6/src/kernel/grompp.c, line: 1593

Fatal error:
There were 47 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

During visualization of the complex.gro file I didnt observe any
distortions in the geometry of heme-cytochrome complex (it looks like NMR
structure) but why that errors occured ?


James

2013/4/3 James Starlight 

> sorry it was mistake :)
>
> assuming that heme is covalently bonded to the cytochrome by means of 2
> cysteines how should I define such bindings (assuming that heme is part of
> my protein) based onb the charmm parameters ?
> its not clear for me why such connection is absent in the residue.dat
> (having HEME included in the rtps)
>
> I still need a example of properly parametrized hem complexed with any
> cytochrome :)
>
> James
>
>
> 2013/4/3 James Starlight 
>
>> hmm
>>
>> I've done parametrization of the hem using standart charmm36 parameters
>> but indeed there is some confusing with the hydrogens
>>
>> for example my pdb (obtained from NMR structure) consist of 2 extr

Re: [gmx-users] Simulation of the HEM-containing proteins

[James Starlight]

sorry it was mistake :)

assuming that heme is covalently bonded to the cytochrome by means of 2
cysteines how should I define such bindings (assuming that heme is part of
my protein) based onb the charmm parameters ?
its not clear for me why such connection is absent in the residue.dat
(having HEME included in the rtps)

I still need a example of properly parametrized hem complexed with any
cytochrome :)

James

2013/4/3 James Starlight 

> hmm
>
> I've done parametrization of the hem using standart charmm36 parameters
> but indeed there is some confusing with the hydrogens
>
> for example my pdb (obtained from NMR structure) consist of 2 extra
> hydrogens (which both parts of the methyl groups) which are not present in
> the rtp parameters. So if I delete both of that hydrogens from pdb- my HEM
> will be -2 charged. On tyhe other hands hem in my pdb lack of 2 protons in
> the COOH groups. Could someone provide me with the HEM (in planargeometry)
> parametrized in charmm36 ?
>
> By the way assuming that the HEM itself is not covalently bonded to the
> rest of the protein ( as in the case of GFP or rhodopsin). So the
> parameters for the hem should be included as the any other diffusiable
> ligand (as the separate itp file) in topology, should'n it?
>
> James
>
>
>
> 2013/4/3 Justin Lemkul 
>
>> On Wed, Apr 3, 2013 at 8:24 AM, James Starlight > >wrote:
>>
>> > Dear Gromacs users!
>> >
>> >
>> > I want to simulate Cytochrome C in complex with HEM using NMR full-atom
>> > structure of that protein as the starting conformation and charm36 force
>> > field's parameters.
>> >
>> > in the charm36 ff I've found parameters for HEM but I have not found
>> params
>> > for the hydrogens (in the aminoacids.hdb file) as well as definition of
>> the
>> > HEM as the part of the protein in the residuetypes.dat ( including
>> > connection to the rest of polypeptide chain ).
>> >
>> > So during pdb2gmx parametrisation I've obtained errors like
>> >
>> > WARNING: atom HA is missing in residue HEME 105 in the pdb file
>> >  You might need to add atom HA to the hydrogen database of
>> building
>> > block HEME
>> >  in the file aminoacids.hdb (see the manual)
>> >
>> >
>> > WARNING: atom HB is missing in residue HEME 105 in the pdb file
>> >  You might need to add atom HB to the hydrogen database of
>> building
>> > block HEME
>> >  in the file aminoacids.hdb (see the manual)
>> >
>> >
>> > WARNING: atom HC is missing in residue HEME 105 in the pdb file
>> >  You might need to add atom HC to the hydrogen database of
>> building
>> > block HEME
>> >  in the file aminoacids.hdb (see the manual)
>> >
>> >
>> > WARNING: atom HD is missing in residue HEME 105 in the pdb file
>> >  You might need to add atom HD to the hydrogen database of
>> building
>> > block HEME
>> >  in the file aminoacids.hdb (see the manual)
>> >
>> >
>> > Have anybody such missing parameters?
>> >
>> >
>> There aren't missing parameters, per se.  The parameters are all there in
>> the .rtp and other force field files.  You just need to construct an .hdb
>> entry for HEM, as pdb2gmx says.  See the manual, section 5.6.4.
>>
>> -Justin
>>
>> --
>>
>> 
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540)
>> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
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[gmx-users] FW: No subject

[Wholly Peach]

http://www.satoriholistichealth.com/uws/wd.fto?ntw

  
 



Wholly Peach





























































  4/3/2013 2:39:18 PM
 






















rl
 
4/3/2013 2:39:18 PM 
Wholly Peach
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Re: [gmx-users] Re: gromacs 4.6.1 on win7?

[Mark Abraham]

Does other compiling with these compilers work?

Mark

On Wed, Apr 3, 2013 at 10:12 AM, 라지브간디  wrote:

> Dear gmx,
>
>
> I have tried in both (32 and 64 bit cygwin) format in my win7 -64 bit
> system but both gave me the compiler gcc-broken as follows :
>
>
> -- Check for working C compiler: /usr/bin/gcc-4.exe -- broken (32 bit)
>
> -- Check for working C compiler: /usr/bin/gcc.exe -- broken (64 bit)
>
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
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>
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Re: [gmx-users] Simulation of the HEM-containing proteins

[James Starlight]

hmm

I've done parametrization of the hem using standart charmm36 parameters but
indeed there is some confusing with the hydrogens

for example my pdb (obtained from NMR structure) consist of 2 extra
hydrogens (which both parts of the methyl groups) which are not present in
the rtp parameters. So if I delete both of that hydrogens from pdb- my HEM
will be -2 charged. On tyhe other hands hem in my pdb lack of 2 protons in
the COOH groups. Could someone provide me with the HEM (in planargeometry)
parametrized in charmm36 ?

By the way assuming that the HEM itself is not covalently bonded to the
rest of the protein ( as in the case of GFP or rhodopsin). So the
parameters for the hem should be included as the any other diffusiable
ligand (as the separate itp file) in topology, should'n it?

James


2013/4/3 Justin Lemkul 

> On Wed, Apr 3, 2013 at 8:24 AM, James Starlight  >wrote:
>
> > Dear Gromacs users!
> >
> >
> > I want to simulate Cytochrome C in complex with HEM using NMR full-atom
> > structure of that protein as the starting conformation and charm36 force
> > field's parameters.
> >
> > in the charm36 ff I've found parameters for HEM but I have not found
> params
> > for the hydrogens (in the aminoacids.hdb file) as well as definition of
> the
> > HEM as the part of the protein in the residuetypes.dat ( including
> > connection to the rest of polypeptide chain ).
> >
> > So during pdb2gmx parametrisation I've obtained errors like
> >
> > WARNING: atom HA is missing in residue HEME 105 in the pdb file
> >  You might need to add atom HA to the hydrogen database of
> building
> > block HEME
> >  in the file aminoacids.hdb (see the manual)
> >
> >
> > WARNING: atom HB is missing in residue HEME 105 in the pdb file
> >  You might need to add atom HB to the hydrogen database of
> building
> > block HEME
> >  in the file aminoacids.hdb (see the manual)
> >
> >
> > WARNING: atom HC is missing in residue HEME 105 in the pdb file
> >  You might need to add atom HC to the hydrogen database of
> building
> > block HEME
> >  in the file aminoacids.hdb (see the manual)
> >
> >
> > WARNING: atom HD is missing in residue HEME 105 in the pdb file
> >  You might need to add atom HD to the hydrogen database of
> building
> > block HEME
> >  in the file aminoacids.hdb (see the manual)
> >
> >
> > Have anybody such missing parameters?
> >
> >
> There aren't missing parameters, per se.  The parameters are all there in
> the .rtp and other force field files.  You just need to construct an .hdb
> entry for HEM, as pdb2gmx says.  See the manual, section 5.6.4.
>
> -Justin
>
> --
>
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
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>
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Re: [gmx-users] Simulation of the HEM-containing proteins

[Justin Lemkul]

On Wed, Apr 3, 2013 at 8:24 AM, James Starlight wrote:

> Dear Gromacs users!
>
>
> I want to simulate Cytochrome C in complex with HEM using NMR full-atom
> structure of that protein as the starting conformation and charm36 force
> field's parameters.
>
> in the charm36 ff I've found parameters for HEM but I have not found params
> for the hydrogens (in the aminoacids.hdb file) as well as definition of the
> HEM as the part of the protein in the residuetypes.dat ( including
> connection to the rest of polypeptide chain ).
>
> So during pdb2gmx parametrisation I've obtained errors like
>
> WARNING: atom HA is missing in residue HEME 105 in the pdb file
>  You might need to add atom HA to the hydrogen database of building
> block HEME
>  in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HB is missing in residue HEME 105 in the pdb file
>  You might need to add atom HB to the hydrogen database of building
> block HEME
>  in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HC is missing in residue HEME 105 in the pdb file
>  You might need to add atom HC to the hydrogen database of building
> block HEME
>  in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HD is missing in residue HEME 105 in the pdb file
>  You might need to add atom HD to the hydrogen database of building
> block HEME
>  in the file aminoacids.hdb (see the manual)
>
>
> Have anybody such missing parameters?
>
>
There aren't missing parameters, per se.  The parameters are all there in
the .rtp and other force field files.  You just need to construct an .hdb
entry for HEM, as pdb2gmx says.  See the manual, section 5.6.4.

-Justin

-- 



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


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[gmx-users] Simulation of the HEM-containing proteins

[James Starlight]

Dear Gromacs users!


I want to simulate Cytochrome C in complex with HEM using NMR full-atom
structure of that protein as the starting conformation and charm36 force
field's parameters.

in the charm36 ff I've found parameters for HEM but I have not found params
for the hydrogens (in the aminoacids.hdb file) as well as definition of the
HEM as the part of the protein in the residuetypes.dat ( including
connection to the rest of polypeptide chain ).

So during pdb2gmx parametrisation I've obtained errors like

WARNING: atom HA is missing in residue HEME 105 in the pdb file
 You might need to add atom HA to the hydrogen database of building
block HEME
 in the file aminoacids.hdb (see the manual)


WARNING: atom HB is missing in residue HEME 105 in the pdb file
 You might need to add atom HB to the hydrogen database of building
block HEME
 in the file aminoacids.hdb (see the manual)


WARNING: atom HC is missing in residue HEME 105 in the pdb file
 You might need to add atom HC to the hydrogen database of building
block HEME
 in the file aminoacids.hdb (see the manual)


WARNING: atom HD is missing in residue HEME 105 in the pdb file
 You might need to add atom HD to the hydrogen database of building
block HEME
 in the file aminoacids.hdb (see the manual)


Have anybody such missing parameters?


James
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Re: [gmx-users] 1-4 interactions

[Justin Lemkul]

On 4/3/13 7:49 AM, Liron Cohen wrote:

I am using PME, can you elaborate about the decomposing you mentioned?


The mesh term includes all long-range interactions and is not broken down, even 
in the presence of energygrps in the .mdp file.  Some time ago, someone posted a 
method of several re-runs with custom .tpr files that suggested one could 
determine the individual contributions of different molecules to the mesh, but I 
don't know if anyone ever tried it or if it would even work.


People often measure these so-called "interaction energies," and they can be 
useful in some cases, but no force field has ever been parametrized to guarantee 
that such a number would even make sense.  Interaction energies may provide some 
qualitative insight, but if you want real quantitative metrics of interaction 
strength, you should probably be doing real free energy calculations.


-Justin



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin Lemkul [jalem...@vt.edu]
Sent: Wednesday, April 03, 2013 2:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] 1-4 interactions

On 4/3/13 7:16 AM, Liron Cohen wrote:

After reading the manual and trying to find more information on the mailing 
list. I'm still not sure about this 1-4 interactions, when I want to calculate 
the energy between two groups (lets say one residue and the rest of the 
protein) should I sum everything (including the 1-4 interactions) or should I 
only include the SR interactions.


1-4 interactions are intramolecular and thus should not be included in
intermolecular energies.  If you're using PME, decomposing the long-range
component to the electrostatics term is challenging.

-Justin

--


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


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--


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


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RE: [gmx-users] 1-4 interactions

[Liron Cohen]

I am using PME, can you elaborate about the decomposing you mentioned? 

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin Lemkul [jalem...@vt.edu]
Sent: Wednesday, April 03, 2013 2:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] 1-4 interactions

On 4/3/13 7:16 AM, Liron Cohen wrote:
> After reading the manual and trying to find more information on the mailing 
> list. I'm still not sure about this 1-4 interactions, when I want to 
> calculate the energy between two groups (lets say one residue and the rest of 
> the protein) should I sum everything (including the 1-4 interactions) or 
> should I only include the SR interactions.

1-4 interactions are intramolecular and thus should not be included in
intermolecular energies.  If you're using PME, decomposing the long-range
component to the electrostatics term is challenging.

-Justin

--


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


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Re: [gmx-users] 1-4 interactions

[Justin Lemkul]

On 4/3/13 7:16 AM, Liron Cohen wrote:

After reading the manual and trying to find more information on the mailing 
list. I'm still not sure about this 1-4 interactions, when I want to calculate 
the energy between two groups (lets say one residue and the rest of the 
protein) should I sum everything (including the 1-4 interactions) or should I 
only include the SR interactions.


1-4 interactions are intramolecular and thus should not be included in 
intermolecular energies.  If you're using PME, decomposing the long-range 
component to the electrostatics term is challenging.


-Justin

--


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


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[gmx-users] 1-4 interactions

[Liron Cohen]

After reading the manual and trying to find more information on the mailing 
list. I'm still not sure about this 1-4 interactions, when I want to calculate 
the energy between two groups (lets say one residue and the rest of the 
protein) should I sum everything (including the 1-4 interactions) or should I 
only include the SR interactions.
Thank you!
Liron
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Re: [gmx-users] water models tip3p.gro and spce.gro

[Justin Lemkul]

On 4/3/13 6:26 AM, Ahmet yıldırım wrote:

Dear users,

I will run MD simulations of all water models in Gromacs. I need spce.gro
and tip3p.gro files. How can I find them?



These don't exist within Gromacs.  Since SPC, SPC/E, and TIP3P are all 3-point 
water molecules, just use spc216.gro and equilibrate using the desired model.


-Justin

--


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


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Re: [gmx-users] RE: Position restraints

[Justin Lemkul]

On 4/3/13 2:36 AM, alex rayevsky wrote:

Thank you for responce and explanation!

So is it a good alghorithm to use gromacs genrestr command and then
include this posre.itp file into topology (without any changes) after
insertion of a ligand.itp?



As long as you use a suitable input file for genrestr, e.g. the ligand only. 
Numbering in the position restraint .itp file is based on [moleculetype], so if 
you use a coordinate file that has multiple molecules in it when running 
genrestr, it won't work.


-Justin



Thank you in advance


On 4/2/13 6:07 AM, alex rayevsky wrote:

Dear All!
I have a doubt about the rightness of ligand/molecule integration in the
topology file. I'm using an amber (tleap) or swissparam.ch to build a
topology of the residue (modified trna). Is it neccessary to generate a
position restrain file (genrestr program) for this residue or not? I've
started both dynamics with/without posrestraints on my residue, however I'm
really not sure that my results from both of them are different. But I want
to do everything in right way, so what can you say about this?


Restraints during equilibration are used to prevent unnatural forces from
theunequilibrated solvent and help prevent deformation of the structure.
It's never a bad idea to restrain the whole solute. If I were reading a
paper thatdescribed restraining the whole solute, except for one residue
because it wasspecial or difficult to deal with, I would immediately be
suspicious.

-Justin




--


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


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[gmx-users] water models tip3p.gro and spce.gro

[Ahmet yıldırım]

Dear users,

I will run MD simulations of all water models in Gromacs. I need spce.gro
and tip3p.gro files. How can I find them?

Thanks in advance
-- 
Ahmet Yıldırım
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Re: [gmx-users] g_hbond

[Erik Marklund]

Yes.

On 3 Apr 2013, at 04:07, Nilesh Dhumal  wrote:

> Hello,
> 
> I am calculating the hydrogen bond life time for my system.
> 
> Do program consider the hydrogen bond criteria for calculation of
> autocorrelation function?
> 
> Nilesh
> 
> 
> 
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[gmx-users] Re: gromacs 4.6.1 on win7?

[라지브간디]

Dear gmx,


I have tried in both (32 and 64 bit cygwin) format in my win7 -64 bit system 
but both gave me the compiler gcc-broken as follows :


-- Check for working C compiler: /usr/bin/gcc-4.exe -- broken (32 bit)

-- Check for working C compiler: /usr/bin/gcc.exe -- broken (64 bit)




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