from:"Rausch, Felix"

AW: [gmx-users] Vizualization with VMD: no image appears

2012-11-21 Thread Rausch, Felix

Hi. 

Try to load in a .gro file of your system first. After that, use the "load data 
into molecule" option to load in the .xtc.

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von shch406
Gesendet: Mittwoch, 21. November 2012 17:47
An: gmx-users@gromacs.org
Betreff: [gmx-users] Vizualization with VMD: no image appears

Dear Gromacs users

To visualize my trajectory with VMD I applied trjconv to .xtc trajectory file 
to eliminate water molecules and velocities remaining protein coordinates only.
However, when I load this reduced file to VMD no image on screen appears, 
nevertheless VMD have identified the file as a "Gromacs compress trajectory 
file".
What may be the cause of this?

The corresponding command is as follows:

trjconv -f MT.xtc -o MT.PnoH.xtc skip 1 -n defau.ndx -pbc nojump -novel

where MT.xtc contains ~10 frames, defau.ndx is default groups index file.
Group 2 (Protein-H) was chosen handling dialog.

Merci pour votre collaboration,
Igor Shchechkin




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AW: [gmx-users] Average pressure(npt equilibration) could not reach my desired value

2012-10-18 Thread Rausch, Felix

Hi,

Did you try to plot the system pressure versus the simulation time to see if 
you end up at ~ 300bar? I presume it will take some time to get this high 
pressure and that would influence (i.e. lower) the average value.
Besides of that, I'm not sure how good barostats behave for such very high 
pressure values, but maybe others can comment on that.


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Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Ali Alizadeh
Gesendet: Donnerstag, 18. Oktober 2012 17:23
An: gmx-users
Betreff: [gmx-users] Average pressure(npt equilibration) could not reach my 
desired value

Dear All users

Average pressure(for my npt equilibration) could not reach my desired
value(300 bar desired , average value =279 bar)

Can i continue my npt equilibration in another npt equilibration for reach my 
desired value?


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AW: AW: [gmx-users] question about the minimization

2012-10-18 Thread Rausch, Felix

If you got the same problems with the protein only (and without any 
restraints), I wonder if you have any non-standard residues (i.e. ligands or 
protein modifications) present in your system?
Because a normal protein should work just fine with the parameters you gave us.

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von reising...@rostlab.informatik.tu-muenchen.de
Gesendet: Donnerstag, 18. Oktober 2012 15:28
An: Discussion list for GROMACS users
Betreff: Re: AW: [gmx-users] question about the minimization

Hi Justin,
I am sorry, I switched the radius and the numbers:
radius=0
charge=1
mass=1

But I already tried it without the membrane and there I had the same problem. 
And also when I did not restrained anything. Not even the membrane I got the 
high force and the LINCS warnings.

Of what physical problems do you think?

I already looked at the protein with Pymol and the residue with the high force 
does not in interact with any other.

>
>
> On 10/18/12 8:51 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi Justin,
>>
>> Well I already tried the protein without the membrane and I got the 
>> same result. And I also make sure that I had no error messages during 
>> the preparation runs.
>>
>
> If the protein crashes in the absence of anything else, then likely 
> you have problems with its starting geometry.  Applying restraints 
> during minimization is probably causing the clashes to be 
> insufficiently resolved.
>
>> I am using the amber03 force field.
>> My dummy atoms have a radius of 1.00 and a charge of 0.00. And yes 
>> they are non bonded atoms.
>>
>
> Radius of 1.0 nm?  If the crash occurs without these atoms, then it's 
> likely irrelevant, but with particles 10 times the size of normal 
> atoms, you may be asking for trouble.
>
> -Justin
>
>
>>> On 10/18/12 7:05 AM, reising...@rostlab.informatik.tu-muenchen.de
>>> wrote:
 Hi Justin,

 I already read the page you send me.
 And I am sure about the first points. But I am not completely sure 
 about
>>>
>>> Sure about the first five points?  The five suggestions on the page 
>>> I linked are all diagnostic steps.  What did they turn up?
>>>
 the mdp file for the nvt run.

 It looks like this:

 define   = -DPOSRES
 integrator   = md
 dt   = 0.002
 nsteps   = 1
 nstxout  = 0
 nstvout  = 0
 nstfout  = 0
 nstlog   = 1000
 nstxtcout= 0
 nstenergy= 5
 energygrps   = Protein Non-Protein
 nstcalcenergy= 5
 nstlist  = 10
 ns-type  = Grid
 pbc  = xyz
 rlist= 0.9
 coulombtype  = PME
 rcoulomb = 0.9
 rvdw = 0.9
 fourierspacing   = 0.12
 pme_order= 4
 ewald_rtol   = 1e-5
 gen_vel  = yes
 gen_temp = 200.0
 gen_seed = 
 constraints  = all-bonds
 tcoupl   = V-rescale
 tc-grps  = Protein  Non-Protein
 tau_t= 0.1  0.1
 ref_t= 298  298
 pcoupl   = no

>>>
>>> What force field are you using?  What about my questions related to 
>>> your so-called dummy atoms?  What are they and what are their 
>>> parameters?
>>> Your
>>> minimization seemed fine, so there's clearly something wrong with 
>>> the physical model that leads to a crash during MD.  At present, 
>>> there's not enough information to say exactly what.
>>>
>>> -Justin
>>>

 Thank you for your help,
Eva


>
>
> On 10/18/12 6:15 AM, reising...@rostlab.informatik.tu-muenchen.de
> wrote:
>> Hi Erik,
>>
>> my .mdp file looks like this:
>>
>> define  = -DPOSRES
>> integrator  = steep
>> emtol   = 10
>> nsteps  = 3
>> nstenergy   = 1
>> energygrps  = System
>> coulombtype = PME
>> rcoulomb= 0.9
>> rvdw= 0.9
>> rlist   = 0.9
>> fourierspacing  = 0.12
>> pme_order   = 4
>> ewald_rtol  = 1e-5
>> pbc = xyz
>>
>>
>> And yes, I use constraints. I have a membrane represented by 
>> dummy atoms around my protein. They are fixed and I also fixed 
>> the backbone. Or is that a problem.
>>
>
> The EM seems to have worked fine, so we need the .mdp file for 
> NVT, not EM.
> Your membrane representation could be an issue, but I'm not clear 
> on the terminology here.  A "dummy atom" (or virtual site) is a 
> particle with nonbonded parameters but n

AW: [gmx-users] question about the minimization

2012-10-18 Thread Rausch, Felix

Hi Eva,

The change in energy in every step became smaller than the machine precision 
can represent (as is stated in the output). In other words: your system is 
minimized to a very high degree.
A value of 10 for the Fmax is very low for a system like yours, even with a 
pure protein in water system you probably wouldn't hit this value. Furthermore, 
30.000 steps for a minimization seems pretty high to me. 

Cheers,
Felix

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von reising...@rostlab.informatik.tu-muenchen.de
Gesendet: Donnerstag, 18. Oktober 2012 10:56
An: gmx-users@gromacs.org
Betreff: [gmx-users] question about the minimization

Hi everybody,

I have a question about the minimization of my protein. For this minimization I 
fixed the backbone and the membrane atoms which around my protein.

I minimized it 3 steps long but after step 20385 it stops with the
output:

Steepest Descents converged to machine precision in 20385 steps, but did not 
reach the requested Fmax < 10.
Potential Energy  = -8.8805600e+05
Maximum force =  3.2341940e+02 on atom 3050
Norm of force =  2.0930219e+00

I do not see why it can not reach a lower force.

I already looked at the structure with Pymol and there I saw that the atom
3050 is in a loop and do not interact with any other residue.

My .mdp file looks like this:

define  = -DPOSRES
integrator  = steep
emtol   = 10
nsteps  = 3
nstenergy   = 1
energygrps  = System
coulombtype = PME
rcoulomb= 0.9
rvdw= 0.9
rlist   = 0.9
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5
pbc = xyz

Do you see a reason why it can not reach a force lower than 10?

Thank you,
 Eva

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AW: [gmx-users] can we generate .xtc file directly from mdrun?

2012-10-04 Thread Rausch, Felix

Hello Albert,

Yes, the settings you mentioned will give you .trr and .xtc files during mdrun. 
But please watch out, you have a little spelling typo in your message. It is 
nstxtcout.

Cheers,
Felix

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Albert
Gesendet: Donnerstag, 4. Oktober 2012 09:45
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] can we generate .xtc file directly from mdrun?

On 10/04/2012 09:22 AM, rama david wrote:
> Yes -x option ( please see mdrun -h )
> You have  to specify it as the output is optiona l
>
> if you use -deffnm all the output posses the same name ( generally I 
> do these one ) set the mdp file option properly to get appropriate 
> saving  for xtc
>   ( see
> the manual for these one )

Hi

thanks for kind comments. here is what I found

http://manual.gromacs.org/current/online/mdp_opt.html#out

shall I simple turn on the nsxtcout and xtc_precision option on like:

; Parameters controlling output writing
nstxout= 5000; Write coordinates to output file
nstvout= 5000; Write velocities to output file
nstenergy= 1000; Write energies to output .edr file
nstlog= 1000; Write output to .log file

nsxtcout = 5000
xtc_precision = 1000


THX
Albert
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AW: [gmx-users] Adding phosphate to protein

2012-09-03 Thread Rausch, Felix

There is a G43a1 modification available with phosphorylated amino acids in the 
users contribution section of the Gromacs homepage. 
http://www.gromacs.org/Downloads/User_contributions/Force_fields

It was uploaded by Graham Smith and Justin made it compatible with the Gromacs 
4.5.x versions, so maybe this would be a good starting point for your modified 
residue.

Good luck.

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von reising...@rostlab.informatik.tu-muenchen.de
Gesendet: Montag, 3. September 2012 10:07
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] Adding phosphate to protein

I want to add the phosphor first.
And I hoped that there is a program just like the "pdb2gmx" which adds 
hydrogens to the protein.

> You haven't anwsered my question. Did you just want to add the 
> phosphate before starting the simulation or were you hoping for the 
> simulation to do it for you?
>
>
> On 2012-09-03 09:51:12AM +0200,
> reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi,
>> I have my protein without phosphorylations and now I want to 
>> phosphorylate one residue of my protein.
>> Is this possible?
>>
>> Thank you
>>
>> > can you be a bit more specific? Are you expecting to phosphorylate 
>> > the protein along the trajectory or did you want to run continuous
>> simulations
>> > with different phosphorylation states?
>> >
>> >
>> > On 2012-09-03 09:30:58AM +0200,
>> > reising...@rostlab.informatik.tu-muenchen.de wrote:
>> >> Hi everybody,
>> >>
>> >> I want to add a phosphate to my protein. Is this possible with
>> gromacs?
>> >>
>> >> Thank you
>> >>
>> >> --
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>> > Programmer/Analyst | KAUL 752A
>> > Genetics, Div. of Research | 705 South 20th Street
>> > p...@uab.edu   | Birmingham AL 35294-4461
>> > (205) 690-0808 |
>> > ==
>> >
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> (205) 690-0808|
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AW: [gmx-users] a residue move in extremely large scale in MD

2012-08-08 Thread Rausch, Felix

That's hard to judge for everyone but you, because there are too many questions 
left. What kind of residue is it? Is it at one of the protein termini, is it on 
the surface or buried by other sections? Are there interactions with other 
parts of the system? Did you check the RMSD or RMSF-values for this residue and 
the protein in general? What exactly does "extremely large" mean? ...
Of course, if the re-centering of the trajectories worked well then these 
observations should have a reason. Maybe it would be helpful to start the 
simulation again with a slightly different starting conformation to exclude a 
simulation artifact of some kind.

Cheers,
Felix

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Acoot Brett
Gesendet: Mittwoch, 8. August 2012 09:00
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] a residue move in extremely large scale in MD

Dear Catch ya,
 
I have watched the trajectory of the simulation. Besdies, I got the PDb file 
for the whole 10 ns MD every 500 ps. Then I compared all the PDB files 
generated, and it confirms that 1 specific residues moves in an extremely large 
space.
 
Can you give me an explaination on it?
 
Cheers,
 
Acoot


- Original Message -
From: Dallas Warren 
To: Discussion list for GROMACS users 
Cc: 
Sent: Wednesday, 8 August 2012 8:58 AM
Subject: RE: [gmx-users] a residue move in extremely large scale in MD

What information has "told you" that you have large scale movement?  Where did 
that information come from, how was it generated?  Have you watch the 
trajectory of this simulation to see how the residue actually moves?

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users- 
> boun...@gromacs.org] On Behalf Of Acoot Brett
> Sent: Wednesday, 8 August 2012 8:30 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] a residue move in extremely large scale in MD
> 
> Dear Marck,
> 
> Will you please give me some suggestions on how to decide whether the 
> probelm is from periodic boundary conditions?
> 
> Cheers,
> 
> Acoot
> 
> 
> - Original Message -
> From: Mark Abraham 
> To: Discussion list for GROMACS users 
> Cc:
> Sent: Monday, 6 August 2012 10:31 PM
> Subject: Re: [gmx-users] a residue move in extremely large scale in MD
> 
> On 6/08/2012 8:58 PM, Acoot Brett wrote:
> >   Dear All,
> >
> > I have a protein with about 400 amino acids. I have done a 
> > production
> MD of it. I find in the 400 amino acids, there is 1 amino acids, 
> during the whole MD process, this residue moves in a extremely large 
> scope in comparison with all the other residues.
> > Do you think this single residue with extremely large-scale movement
> in the whole MD has important biological function, or has no 
> biological function?
> 
> I'd start by proving that it was not a problem with periodic boundary 
> conditions! If real, movement may or may not be indicative of 
> functional significance - the question is impossible to answer out of 
> context.
> 
> Mark
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AW: [gmx-users] Structure optimization failure

2012-06-29 Thread Rausch, Felix

Hi Lara,

with the .mdp you sent you are NOT going to perform a minimization, but a NPT 
equilibration run (i.e. a MD simulation, as stated in the first line). So check 
a tutorial of your choice to get a proper .mdp for a simple energy minimization.

Greetings
Felix

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Lara Bunte
Gesendet: Freitag, 29. Juni 2012 12:03
An: gmx-users@gromacs.org
Betreff: [gmx-users] Structure optimization failure

Hello

I use a CHARMM27 force field and my system is lumiflavin in water. I use the 
spc216 water model, a dodecahedral box with 1.3 nm. I want to make a structure 
minimization. I made a file pr.mdp. Could you please tell me, what I could do 
better in this file, or what is wrong? I guess there has to be something wrong, 
because GROMACS failed with grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr 
with the error: "Water molecule starting at atom 3924 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
"


My pr.mdp file is:


title   = lumiflavin NPT equilibration define  = -DPOSRES  ; 
position restrain the protein

; Run parameters
integrator  = md    ; leap-frog integrator nsteps  = 
5 ; 2 * 5 = 100 ps dt  = 0.002 ; 2 fs

; Output control
nstxout = 5000  ; save coordinates every 4 ps nstvout = 
5000  ; save velocities every 4 ps nstenergy   = 5000  ; 
save energies every 4 ps nstlog  = 5000  ; update log file 
every 4 ps


; Bond parameters
continuation    = yes   ; Restarting after NVT constraint_algorithm = 
lincs    ; holonomic constraints constraints = all-bonds ; all bonds 
(even heavy atom-H bonds) constrained lincs_iter  = 1 ; 
accuracy of LINCS lincs_order = 4 ; also related to accuracy

; Neighborsearching
ns_type = grid  ; search neighboring grid cells nstlist 
= 10 ; edited to 1 rlist   = 1.0   ; short-range 
neighborlist cutoff (in nm) rcoulomb    = 1.0   ; short-range 
electrostatic cutoff (in nm) rvdw    = 1.0   ; short-range van 
der Waals cutoff (in nm)

; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics pme_order   = 4 ; cubic interpolation 
fourierspacing  = 0.12  ; grid spacing for FFT

; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat tc-grps 
= Isoalloxazin Sol   ; two coupling groups - more accurate tau_t   = 
0.1   0.1 ; time constant, in ps ref_t   = 300   300 ; 
reference temperature, one for each group, in K

; Pressure coupling is on
pcoupl  = berendsen ; Pressure coupling on in NPT pcoupltype  = 
isotropic ; uniform scaling of box vectors tau_p   = 2.0   
; time constant, in ps ref_p   = 1.0   ; reference pressure, in 
bar compressibility = 4.5e-5    ; isothermal compressibility of water, 
bar^-1 refcoord_scaling = all

; Velocity generation
gen_vel = yes    ; assign velocities from Maxwell distribution 
gen_temp    = 300   ; temperature for Maxwell distribution gen_seed    = 
-1    ; generate a random seed


Thank you for helping me
Greetings
Lara

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AW: [gmx-users] membrane simulation

2012-05-03 Thread Rausch, Felix


Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Anirban Ghosh
Gesendet: Donnerstag, 3. Mai 2012 13:39
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] membrane simulation


On Thu, May 3, 2012 at 4:38 PM, 
mailto:scapr...@uniroma3.it>> wrote:
Hi all,
I'm new in Membrane simulations with Gromacs. I have to simulate a system
made up of a protein just leant on a membrane patch which has previously
been extended and made it free of periodicity (with trjconv). I'm reading
the "KALP15 in DPPCI" Tutorial and, so far, I managed to obtain my protein
(in pdb code) very close to the membrane surface by using editconf and cat
command. At this point, I don't know how to get on. 1)How should I
generate the topology file which includes  the coordinates both of the
protein and of the membrane?

If you are using the ff53a6 FF then you need to add the appropriate lipid 
parameters in the ffnonbonded.itp and ffbonded.itp files (of ff53a6 FF) files 
which is very well explained in the tutorial. Then in your .top file you need 
to include the DPPC.itp. However, if you are using CHARMM36 FF, then you can 
directly use pdb2gmx on your system (I suppose DPPC is already included in it). 
If you wish to use the ff43a1 FF, then you can find the modified .itp files at 
https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial .

2)Furthermore, the lipid molecules are listed in my pdb file  with the
abbreviation "DPP", whereas I see that those ones are called "DPPC" in the
Tutorial. Therefore, Should I replace "DPP" abbreviation with "DPPC" in my
pdb file? Could this difference cause any bugs in the next steps?

PDB files use three letter convention for residue names. I think you can change 
them without any issue in the .gro file.

-Anirban


You can also simply replace DPP by DPPC in the pdb. But be careful that there 
is no shifting of the columns after the residue name, i.e. it should *NOT*look 
like this

ATOM  1  C1  DPP 1  17.610  52.750  30.500  1.00  0.00
ATOM  2  C2  DPPC 1  16.160  50.940  30.040  1.00  0.00
ATOM  3  C3  DPPC 1  18.640  50.520  29.970  1.00  0.00
ATOM  4  N4  DPP 1  17.520  51.490  29.680  1.00  0.00


Any suggestion would be appreciated,

Silvia

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AW: [gmx-users] Gromos87

2012-04-12 Thread Rausch, Felix

Hi Shima,

It would be number 17, but as you can see on the prefix, its deprecated (in 
other words outdated) and should not be used anymore (unless you really have to 
for some reason). Why not try a more modern force field?

Cheers,
Felix

Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Shima Arasteh
Gesendet: Donnerstag, 12. April 2012 17:09
An: Discussion list for GROMACS users
Betreff: [gmx-users] Gromos87

Dear friends,

I'd like to use gormos87 force field in my simulation. Which force field am I 
supposed to select?

 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (with CMAP) - version 2.0
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15: [DEPRECATED] Encad all-atom force field, using full solvent charges
16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
17: [DEPRECATED] Gromacs force field (see manual)
18: [DEPRECATED] Gromacs force field with hydrogens for NMR

Thanks in advance,
Shima
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AW: [gmx-users] Residue 'FOR' not found in residue topology database

2012-04-12 Thread Rausch, Felix

Hi Shima,

It seems like this residue is not parameterized for the force field you want to 
use. Maybe check 
http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks if 
you can find it under a different name. If not, have a look at 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field.

Cheers,
Felix

Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Shima Arasteh
Gesendet: Donnerstag, 12. April 2012 09:43
An: Discussion list for GROMACS users
Betreff: [gmx-users] Residue 'FOR' not found in residue topology database

Dear Gromacs friends,

I attached my .pdb file in this message, as you see, I have formyl residue in 
it. I'd like to get a .gro output of it by using this commands, but getting the 
fatal error:

# pdb2gmx -f glc.pdb -o glc.gro -ignh -ter -water spc

Fatal error:
Residue 'FOR' not found in residue topology database

How can I solve this problem?

Thanks ,
Shima



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AW: [gmx-users] Shape of box

2012-04-04 Thread Rausch, Felix

Hi Lara,

Please see "editconf -h" for the available box shapes. Which of these you use 
is depending on your system (or a matter of taste actually).
The dodecahedron is mostly used to decrease the system volume, thus it's a good 
choice for the simulation of a single protein in solvent (as in your tutorial?).

Cheers,
Felix

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Lara Bunte
Gesendet: Mittwoch, 4. April 2012 11:24
An: gmx-users@gromacs.org
Betreff: [gmx-users] Shape of box

Hello

If you add solvent water around your protein you have to generate a box with 
the editconf command. How to know what shape that box should have? In my 
tutorial is a dodecahedron used. What other boxes exist and how to know which 
box one has to use?

Thanks
Greetings
Lara

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AW: [gmx-users] the mdrun "-v"

2012-04-02 Thread Rausch, Felix

Hey Acoot,

The “–v” option simply means “verbose”, so mdrun outputs a bit more information 
(for example a nice finish time estimation) than it would do without “-v”. I 
doubt that giving a little bit more output to the console will influence the 
run time significantly. My advice: Just try it out ;)

Cheers,
Felix

Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Acoot Brett
Gesendet: Dienstag, 3. April 2012 08:19
An: Discussion list for GROMACS users
Betreff: [gmx-users] the mdrun "-v"


Dear All,

For the function of mdrun. will you please introduce the time difference for 
the whole mdrun with or without "-v"? I suppose with "-v" will need some 
calculation time, but I am not sure whether the time spent is significant.

Cheers,

Acoot
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AW: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread Rausch, Felix

Hello again,

Well, I once had problems with simulations crashing randomly during production 
runs (sometimes after tens of nanoseconds) with the LINCS warnings you 
described. Switching LINCS from "all-bonds" to only "h-bonds" did the trick for 
me, although I never exactly figured out why. 
Maybe it's worth a try for you, too?
Cheers,
Felix

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von francesca vitalini
Gesendet: Donnerstag, 29. März 2012 15:15
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] Not able to continue with Equilibration

Hi!
I'm having a similar problem. I have a dimer solvated in a big box of water 
plus ions that I have managed to minimize correctly (see output of minimization 
at the end) but when I try to run NVT equilibration (see later) I get LINCS 
warnings(see below) refearred to atoms which are not in a cluster or in a 
strange position. I have added dihedral restraints on them but still the same 
type of error. I'm using GROMACS 3.3.1. I have tried to switch to a newer 
version of GROMACS but still the same error.
Does anyone have any suggestions?
Thanks
Francesca


MINIMIZATION OUTPUT

Steepest Descents converged to Fmax < 1000 in 681 steps Potential Energy  = 
-1.9597512e+07
Maximum force =  2.4159846e+02 on atom 13087
Norm of force =  2.1520395e+04


MINIMIZATION.MDP

define = -DEFLEXIBLE ; flexible water
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 1000.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm
emstep  = 0.001  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization)
steps to perform

; 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
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   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)


NVT.MDP

define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1 ; 2 * 1 = 20 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 50; save coordinates every 0.2 ps
nstvout = 50; save velocities every 0.2 ps
nstenergy   = 50; save energies every 0.2 ps
nstlog  = 50; update log file every 0.2 ps
; Bond parameters
unconstrained_start = no
;continuation   = no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 3.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 3.0   ; short-range electrostatic cutoff (in nm)
rvdw= 3.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = berendsen ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one
for each group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

; Dihedral restraints

dihre   =  simple ; Some dihedrals are restrained  for
instance peptide bonds are set to trans conformation.
dihre_fc=  500
dihre_tau   =  0.0
nstdihreout =  50

NVT LINCS ERROR

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.002851 (between atoms 10721

AW: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread Rausch, Felix

Hello,

The results of the energy minimization look reasonable. Nevertheless, you 
should (visually) check your equilibration starting structure for problems 
(e.g. clashes that could not be solved by EM). It would be a good idea to 
concentrate on the atom numbers given in the error messages.

To prevent the "exploding" system during equilibration, reducing the time step 
may be a good idea. Or you could start with a short NVT run first to 
equilibrate the temperature before switching to NPT. Furthermore, the coupling 
of ions in a single thermostat group is in general not a good idea (search the 
mailing list for many discussions about this topic).

Good luck.

Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Hendry
Gesendet: Donnerstag, 29. März 2012 11:25
An: Discussion list for GROMACS users
Betreff: [gmx-users] Not able to continue with Equilibration

Hi,

I am using Gromacs 4.5.4. After successful minimization by SD, I continued with 
equilibration step but I got the below errors. I tried many times with 
different parameters but the problem still persists. I have given errors and md 
parameters of equilibration step below. I have also provided my minimization 
output at the end. Could you provide some suggestions what went wrong?.

Many thanks

Sincerely
Hendry

Errors:
Warning: 1-4 interaction between 2969 and 2974 at distance 5.543 which is 
larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 92.242942, max 9194.071289 (between atoms 3025 and 3024)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2987   2973  106.31.3892   7.3433  0.1530
   2974   2973  174.81.1940   7.7482  0.1530
   2975   2974   79.90.1865   1.4460  0.1530
   2978   2975   98.50.1423   0.6164  0.1390
   2982   2978   86.10.1421   0.6512  0.1390
   2979   2978   89.80.1114   5.2456  0.1090
   2989   2987  132.20.1781   2.6697  0.1330
   2988   2987  142.20.2284   2.7180  0.1230
   2971   2969   62.97.0921   3.5084  0.1330
   2970   2969   88.16.8598   4.7791  0.1230
   2973   2971  120.62.8109   8.8274  0.1470
   2972   2971  165.62.0293   6.9953  0.1000
   3016   3013  103.10.5628  65.6450  0.1390
   3014   3013   39.00.3331   5.0018  0.1330
   3017   3014   81.60.1827  57.9252  0.1330
   3015   3014   77.90.0752   6.3613  0.1090
   3020   3016   81.32.2255  79.7378  0.1390
   3019   3016  100.90.4862  54.4883  0.1390
   3019   3017   79.30.1679  57.8415  0.1330
   3018   3017   94.50.1686  66.3440  0.1000
   3022   3019   87.70.5657   7.7539  0.1390
   3026   3022  104.50.8085  54.9923  0.1390
   3023   3022   87.40.6108   5.0641  0.1090
   2968   2964  174.11.5617   5.1413  0.1470
   2965   2964   59.55.2178   4.0658  0.1470
   2969   2965   35.57.6693   2.9000  0.1530
   2966   2965  137.35.3225   4.6157  0.1530
   2967   2966  150.31.6016   1.7332  0.1530
   2968   2967   72.40.1685   1.8310  0.1530
   3026   3024   94.80.8572  96.6156  0.1390
   3025   3024   89.90.6811 1002.2628  0.1090
   3027   3026  108.01.1638  47.5384  0.1090
   2991   2989  138.20.2045   0.6556  0.1470
   2990   2989  157.00.1236   0.7213  0.1000
   2998   2991   89.90.1961   0.9471  0.1530
   2992   2991   79.50.1931   0.5434  0.1530
   2993   2992   49.80.1577   0.1862  0.1530
   3000   2998   84.90.1463   0.5492  0.1330
   2999   2998   83.30.1346   0.5372  0.1230
   3002   3000   44.20.1535   0.2150  0.1470
   3003   3002   31.60.1548   0.1834  0.1530
   3009   3007   62.40.1507   0.3181  0.1330
   3008   3007   44.10.1280   0.1578  0.1230
   3011   3009   80.30.2401   1.9894  0.1470
   3010   3009   82.90.1141   0.3157  0.1000
   3028   3011   85.20.2391   1.9233  0.1530
   3012   3011   97.90.3034   4.9831  0.1530
   3013   3012   82.40.3759   7.3991  0.1530
   3024   3020   85.62.4674  98.3412  0.1390
   3021   3020   81.01.2452  66.1375  0.1090
   3030   3028   88.90.1492   0.2673  0.1330
   3029   3028   61.20.1379   0.2407  0.1230
  49372  49371   89.50.1000 221.0566  0.1000
  49373  49371   92.40.1000 170.7231  0.1000
   2956   2954  153.40.1550   3.5621  0.1470
   2955   2954  135.50.1246   0.8967  0.1000
   2962   2956   76.60.7151   5.0532  0.1530
   2957   2956  178.70.1220   3.9773  0.1530
   2958   2957  155.0

AW: [gmx-users] About movie in GROMACS

2012-03-28 Thread Rausch, Felix

Hi.

Take a look at the "-center" flag of trjconv. Together with "-pbc" (and maybe 
also "-ur") it should be possible to center your molecules of interest in the 
middle of the simulation cell.


Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von rama david
Gesendet: Donnerstag, 29. März 2012 07:18
An: Discussion list for GROMACS users
Betreff: [gmx-users] About movie in GROMACS

HI Gromacs Friends,
 I complete one simulation for 4 different molecule  placed apart
in box of  dimension 4 4 4 ..
when I used the trajectory I saw the one molecule interact with each other but 
they are
getting broken because of box..(Some part protruding from other side).
To see movie I used the command
1. trjconv -s ..tpr  -f ..xtc  -o movie.pdb -pbc nojump -dt 10
 The molecules moving apart without any interaction

2. trjconv -s ..tpr  -f ..xtc  -o movie.pdb -pbc whole -dt 10
 The molecules are interacting in cell ..
  but because of periodic cell , near the cell boundary  the molecule
 interaction get remove and molecules come in cell from other side..
( I know it is because of periodic boundary condition ..one goes from right
  hand side come in cell through left hand side )

To see the four molecule interacting each other near also cell boundary , what 
command
I have to use ???
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AW: [gmx-users] Information on .mdp files

2012-03-15 Thread Rausch, Felix

Hey.

Well, it's always good to check the online documentation for such things.

http://www.gromacs.org/Documentation/File_Formats/.mdp_File

There you should find all information you need. Including examples and all 
usable keywords sorted by topic/task.

Good luck,
Felix

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Lara Bunte
Gesendet: Donnerstag, 15. März 2012 16:24
An: gmx-users@gromacs.org
Betreff: [gmx-users] Information on .mdp files

Hello
I want to learn how to create a .mdp file and learn what I can write in such a 
file and learn what the entries in this file are meaning. 

I did not find this in the manual. Could you please give me link or some source 
where I can find this information?

Thanks and best greetings
Lara

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AW: [gmx-users] problem in creating forcefield.doc

2012-01-23 Thread Rausch, Felix

Hi.

You don't have to paste anything in there. Take an empty text document and
write the text you like to name your force field like into the first line.
For example this

GROMOS 53A6 forcefield , extended to include Berger force field parameter.

Save it as forcefield.doc. That's all.

Good luck!

Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im
Auftrag von Anushree Tripathi
Gesendet: Montag, 23. Januar 2012 08:52
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] problem in creating forcefield.doc

I have created one file named it as "forcefield.doc" and paste the contents of
"forcefield.itp" into it and also include "lipid.itp file.The content of my
"forcefield.doc" file is given below:

#define _FF_GROMOS96
#define _FF_GROMOS53A6

[ defaults ]
; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ
11no1.01.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "lipid.itp"

Let me know whether it is correct or not.
On Mon, Jan 23, 2012 at 12:17 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:
On 23/01/2012 5:13 PM, Anushree Tripathi wrote:

I am using gromacs 4.5.3 version and I am trying to follow the tutorials. For

starting I am following the *KALP15 in DPPC*

tutorial(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html).

I am not getting the point that is given below :

Next, create a forcefield.doc file that contains a description of the force
field parameters in it. Mine contains something like:

GROMOS 53A6 forcefield , extended to include Berger force field parameter.

Please guide me for creating forcefield.doc.

Have a look at the contents of this file in the pre-supplied force fields. Then
look at the normal output of pdb2gmx. The former is used in the latter to help
you pick the force field you want to use.

Mark

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AW: [gmx-users] Regarding trajectory file

2012-01-18 Thread Rausch, Felix

Or you could use trjconv in a little script to convert the snapshots you
like to  .pbd. Use the -b and -e flags to choose the respective time
points.

Also see
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
for the use trjconv non-interactively.

 

Good luck.

 

Von: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] Im Auftrag von aiswarya pawar
Gesendet: Mittwoch, 18. Januar 2012 07:53
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] Regarding trajectory file

 

You can write this on VMD forum. Anyways you can try by doing this in
the Tcl console-

set sel [atomselect top "solvent"]
$sel get {x y z}

This would give you the coordinates of the solvent, for your purpose you
got to iterate so as to get  for each time step.


Aiswarya
SERC Dept, IISc
Bangalore




On Wed, Jan 18, 2012 at 12:06 PM, Mark Abraham 
wrote:

On 18/01/2012 5:31 PM, Ravi Kumar Venkatraman wrote:


Dear All,
I have ran a 10 ns production run for chloranil in 500
methanol solvent box. I want to get the coordinates of solvent and
solute at different time steps from the trajectory file (*.xtc). Can
anybody tell me how to extract the details using VMD or any other
viewer.

 

You're unlikely to get help for non-GROMACS software on this mailing
list. Check out manual section 7.4 for clues on what GROMACS tools might
help, and then section 8 and appendix D for more details.

Mark
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Re:[gmx-users]-Snapshots

2012-01-10 Thread Rausch, Felix

 

Hi.

 

You will need a visualization program like VMD to get a 3D
representation of your system. After reading in the .gro file, you can
edit representation details and take pictures. 

 

Greetings,

Felix

 

Von: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] Im Auftrag von cuong nguyen
Gesendet: Dienstag, 10. Januar 2012 07:39
An: jalem...@vt.edu; Discussion list for GROMACS users
Betreff: Re: [gmx-users]-Snapshots

 

Thanks a lot Justin. I have just used trjconv -dump with the command
"trjconv -s NVT_final2ns.tpr -f NVT_final2ns -o trjconv.gro -dump 1" to
extract a frame. However, I still do not know how to get the snapshot
like a 3D picture
 .
Please help me!

Many thanks

Cuong Nguyen

2012/1/10 Justin A. Lemkul 



cuong nguyen wrote:

Dear Users,

Please let me know if we can get snapshot from GROMACS. I am using
version 4.4.

 

The final configuration of any simulation is written to a coordinate
file by default.  You can extract any frame from your trajectory using
trjconv -dump.

-Justin

-- 


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


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-- 

Nguyen Van Cuong

PhD student - Curtin University of Technology

Mobile: (+61) 452213981

 

 

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AW: [gmx-users] Bond force constant for GROMOS

2011-07-06 Thread Rausch, Felix

Hey Javier,
 
Thank you very much!
 
I already read the manual, but somehow didn't get the point. Now its clear, 
thanks.
 
Felix



Von: gmx-users-boun...@gromacs.org im Auftrag von Javier Cerezo
Gesendet: Mi 06.07.2011 09:40
An: gmx-users@gromacs.org
Betreff: Re: [gmx-users] Bond force constant for GROMOS


Hi Felix

Take a look to 4.2.1 section in the manual. Gromos force constants (k^b) has 
this extra nm-2 factor because they are defined as: 
2 k^b bij^2 = k^{b,harm}  (equation 4.39 in the manual version 4.5.4)

So you have to divide your derived harmonic force constants (in KJ/(mol*nm^2) 
by 2 and bij^2 (equilibrium distance or ideal bond length as stated in gromos 
files) to get the gromos one (k^b). It could also be useful for you to visit 
the new GROMOS website as there is some free downloadable FF documentation.

Javier

El 06/07/11 08:48, Rausch, Felix escribió: 

Dear Gromacs-users,
 
I would like to add a new bond type to the ffbonded.itp of the 
Gromos53a6 force field. For that, I tried to obtain the force constant for my 
new bond by performing vibrational frequency calculations with Gaussian. With 
that, I obtained the force constant in mDyne/A.
My problem is now: How can I convert this value to kJ/(mol*nm(4)) as 
required for the force field? I already tried, but I only end up at 
kJ/(mol*nm(2)). Also arround the web I could only find a factor for conversion 
of mDyne/A to kJ/(mol*nm(2)). Is there any trick or hint you can give me about 
that?
 
Thanks for your help,
Felix
  


-- 
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Mua
Murcia (Spain)
Tlf.(+34)868887434
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[gmx-users] Bond force constant for GROMOS

2011-07-06 Thread Rausch, Felix

Dear Gromacs-users,
 
I would like to add a new bond type to the ffbonded.itp of the Gromos53a6 force 
field. For that, I tried to obtain the force constant for my new bond by 
performing vibrational frequency calculations with Gaussian. With that, I 
obtained the force constant in mDyne/A.
My problem is now: How can I convert this value to kJ/(mol*nm(4)) as required 
for the force field? I already tried, but I only end up at kJ/(mol*nm(2)). Also 
arround the web I could only find a factor for conversion of mDyne/A to 
kJ/(mol*nm(2)). Is there any trick or hint you can give me about that?
 
Thanks for your help,
Felix
  
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Re: [gmx-users] where can I download POPC membrane file?

2011-05-30 Thread Rausch, Felix

Ah okay. Sorry then.
 
But if its only the atom names that dont match, isn't it worth a try to either 
name them correctly in the pdb file(maybe via a little script) or to adjust the 
names in the topology file so they match the pdb? (I know, very simple-hearted 
question.)
 



Von: gmx-users-boun...@gromacs.org im Auftrag von albert
Gesendet: Mo 30.05.2011 09:37
An: Discussion list for GROMACS users
Betreff: Re:AW: Re: [gmx-users] where can I download POPC membrane file?


I know this, but this file cannot be used because the atom name is quite 
different from gromacs CHARMM36 topol library.



At 2011-05-30,"Rausch, Felix"  wrote:


Check this link given by another (unknown) mailing list user yesterday 
(Topic name: about POPC in Gromacs )!
 
http://terpconnect.umd.edu/~jbklauda/research/download.html 
<http://terpconnect.umd.edu/%7Ejbklauda/research/download.html> 



Von: gmx-users-boun...@gromacs.org im Auftrag von albert
Gesendet: So 29.05.2011 21:23
An: Discussion list for GROMACS users
Betreff: Re:Re: [gmx-users] where can I download POPC membrane file?


But I don't think it is pre-equilibrium POPC membrane.. and more 
over, the position from VMD is not pre-aligned with OPM database. It would be a 
great problem for putting our protein in the membrane.. 




At 2011-05-30,"Sergio Manzetti"  wrote:


You can build it using VMD (VIsual Molecular Dynamics)




2011/5/30 albert 


Dear all:

  I would like to use charmm36 and POPC for membrane 
protein simulation. and I am wondering where can I download charmm36 
pre-pribriumed POPC PDB and topol file for gromacs?

Thank you very much
Best

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AW: Re: [gmx-users] where can I download POPC membrane file?

2011-05-30 Thread Rausch, Felix

Check this link given by another (unknown) mailing list user yesterday (Topic 
name: about POPC in Gromacs )!
 
http://terpconnect.umd.edu/~jbklauda/research/download.html



Von: gmx-users-boun...@gromacs.org im Auftrag von albert
Gesendet: So 29.05.2011 21:23
An: Discussion list for GROMACS users
Betreff: Re:Re: [gmx-users] where can I download POPC membrane file?


But I don't think it is pre-equilibrium POPC membrane.. and more over, the 
position from VMD is not pre-aligned with OPM database. It would be a great 
problem for putting our protein in the membrane.. 




At 2011-05-30,"Sergio Manzetti"  wrote:


You can build it using VMD (VIsual Molecular Dynamics)




2011/5/30 albert 


Dear all:

  I would like to use charmm36 and POPC for membrane protein 
simulation. and I am wondering where can I download charmm36 pre-pribriumed 
POPC PDB and topol file for gromacs?

Thank you very much
Best

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[gmx-users] MG-ATP

2011-04-27 Thread Rausch, Felix

Hi.
 
Looking at the list of building blocks available in GROMACS 
(http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks?highlight=building+blocks)
 you can find ATP as well as MG. So having a ATP-MG-complex in your simulation 
shouldn't be a problem.
 
Regards,
Felix



Von: gmx-users-boun...@gromacs.org im Auftrag von Sajad Ahrari
Gesendet: Mi 27.04.2011 10:52
An: gromacs user forum
Betreff: [gmx-users] MG-ATP


dear users
is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG, apart 
from each other and not being crystallized in the right place. can i omit them 
and replace ADP's with MG-ATP? or I should introduce this topology to gromacs?
regards
sajad 
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[gmx-users] Fw: trjconv -pbc and broken reside

2011-04-27 Thread Rausch, Felix

You could try
 
trjconv -f -s -pbc res -ur compact -center -o
 
Good luck.



Von: gmx-users-boun...@gromacs.org im Auftrag von ana johari
Gesendet: Mi 27.04.2011 08:55
An: gmx-users@gromacs.org
Betreff: [gmx-users] Fw: trjconv -pbc and broken reside


dear justin,
Hello,after 5ns MD,based on your recommend, I use" trjconv  -f  -s -pbc -mol 
-center -o *.pdb" command to get the whole protein without any separation,but I 
found some part of the residue was broken,and some new bond at the end of some 
residue was formed.I need the intact molecule for docking,but how should I 
solve this problem.
any advice was appreciate.
tanks,
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Re: [gmx-users] Atomtype CCL4 not found

2011-03-29 Thread Rausch, Felix

I suppose the term "CCL4" is contained somewhere in the files you use (.top or 
#included .itp). So dont search in the force field folder but in your working 
directory. If you found the occurence, replace it with CCl4.
For further help it would be better to know the exact error message and/or info 
what you are trying to do.
 
Good luck.
Felix



Von: gmx-users-boun...@gromacs.org im Auftrag von ahmet yildirim
Gesendet: Di 29.03.2011 15:35
An: jalem...@vt.edu; Discussion list for GROMACS users
Betreff: Re: [gmx-users] Atomtype CCL4 not found


Dear Justin,


There is "CCl4  12.011   ; carbon in carbontetrachloride (solvent)" in the 
gromos43a1.ff/atomtypes.atp file. 
But I still have the error "Atomtype CCL4 not found".


2011/3/29 Justin A. Lemkul 




ahmet yildirim wrote:


Dear users,

Force field: 43a1
water model: spc

After this command:grompp -f em.mdp -p topol.top -c 
solvated.gro -o em.tpr

I have the following error:

Fatal error:
Atomtype CCL4 not found

What should I do?




Use an appropriate atom type.  The issue is probably capitalization 
somewhere, i.e. CCl4 rather than CCL4.  See atomtypes.atp.

-Justin




-- 
Ahmet YILDIRIM




-- 


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


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-- 
Ahmet YILDIRIM

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AW: [gmx-users] lipopeptide problem

2011-03-17 Thread Rausch, Felix

If you want the lipid connected to the amino acid, i think it would be a good 
idea to add a new residue type to aminoacids.rtp which contains both, your 
lipid and the amino acid its connected to. You can start from the rtp entry of 
the amino acid and add the lipid parameters. After doing that, you can use 
pdb2gmx to build the topology for the whole system even without any need to 
adjust the .top afterwards. The link you gave is the right place to get a 
"route" for this intent.
 
Good luck.
Felix



Von: gmx-users-boun...@gromacs.org im Auftrag von Emine Deniz Tekin
Gesendet: Mi 16.03.2011 22:53
An: gmx-users@gromacs.org
Betreff: [gmx-users] lipopeptide problem


Hi GROMACS Users,

I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I simulated a 
peptide before but this is the first time I am trying to combine a lipid with a 
peptide (to get a lipo-peptide). I would be really happy if you could help me 
out with the following question 

I am tring to create a louroic acid connected to and an 8-redidue peptide. To 
create residues, I used ARGUSLAB . For the louric acid I used BERGER lipid 
parameters. Then, as described in KALP-15 in DPPC tutorial, I combined 
ffbonded.itp and ffnonbonded.itp with lipid.itp. I also adjusted the topol.top 
files as described in the manual. But this procedure did not yet give me an 
attached louric acid and peptide. I still have to play with the aminoacids.hdb, 
aminoacids.rtp, residuetypes.dat, atomtypes.atp, and specbond.dat files. I 
would appreciate if you could let me know how to modify these files, especially 
the aminoacids.hdb file. I tried several things but it not work. Note that, I 
applied the suggestions in 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, 
but it was not sufficient.

Best regards

Deniz 

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AW: [gmx-users] modified atomtypes.atp and grompp

2011-03-11 Thread Rausch, Felix

Dear Justin,

I checked my working directory (including ff-directory) again and found some 
entries (i added myself) with the old uppercase spelling in the nonbonded.itp. 
After editing these lines everything works well. Conclusion: I have to learn 
using the command grep properly :)

Thank you very much for your help.
Felix

Von: gmx-users-boun...@gromacs.org im Auftrag von Justin A. Lemkul
Gesendet: Fr 11.03.2011 13:07
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] modified atomtypes.atp and grompp

Rausch, Felix wrote:
> 
> Dear Gromacs users,
> 
> I would like so simulate a protein with phosphorylated amino acids with
> Gromacs 4.5.3. To do so, I got the "ffG43a1p" forcefield available from
> the user contributions section (subsection force fields) and adapted the
> parameters given there to Gromos53a6.
> The problem now is that they introduced a new atom type called "OP",
> which I have to add to the atomtypes.atp of my modified force field. I
> already read about problems of a modified atomtypes.atp here in the
> mailing list, but I assumed the problems were sorted out with version 4.5.3.

Not entirely, but probably the post you saw related to an LP atomtype, which
appears to be a special case.

> But if I add OP to the atom list, pdb2gmx works fine, but grompp is
> raising the error
> 
> Program grompp, VERSION 4.5.3.
> Source code file: toppush.c, line: 629
> 
> Fatal error:
> Unknown atomtype CMET
> 
> which is quite strange because  "CMET" isn't appearing in any file I'm
> using. When I remove OP from the atom list, pdb2gmx is of course raising
> an error, so I'm a bit stuck here...
> 

grompp reads all the force field files and is finding something it doesn't like.
  In 4.5.3, the proper capitalization should be "CMet," not "CMET," as it was in
old versions.  Capitalization and other nomenclature has been standardized as of
version 4.5.3, so old files with outdated names cause errors.

-Justin

> To cut a long story short: Is there any way to introduce a new atom type
> to atomtypes.atp or do I have to parameterize the phosphorylated
> residues with already presend atom types? 
> 
> Thank you in advance,
> Felix Rausch
>
> 
>

--

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

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[gmx-users] modified atomtypes.atp and grompp

2011-03-10 Thread Rausch, Felix

 
Dear Gromacs users,
 
I would like so simulate a protein with phosphorylated amino acids with Gromacs 
4.5.3. To do so, I got the "ffG43a1p" forcefield available from the user 
contributions section (subsection force fields) and adapted the parameters 
given there to Gromos53a6. 
The problem now is that they introduced a new atom type called "OP", which I 
have to add to the atomtypes.atp of my modified force field. I already read 
about problems of a modified atomtypes.atp here in the mailing list, but I 
assumed the problems were sorted out with version 4.5.3.
But if I add OP to the atom list, pdb2gmx works fine, but grompp is raising the 
error
 
Program grompp, VERSION 4.5.3.
Source code file: toppush.c, line: 629
 
Fatal error:
Unknown atomtype CMET
 
which is quite strange because  "CMET" isn't appearing in any file I'm using. 
When I remove OP from the atom list, pdb2gmx is of course raising an error, so 
I'm a bit stuck here...
 
To cut a long story short: Is there any way to introduce a new atom type to 
atomtypes.atp or do I have to parameterize the phosphorylated residues with 
already presend atom types?  
 
Thank you in advance,
Felix Rausch

 

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