[gmx-users] Error with polymer surface modeling

[h a]

Dear users,

I'm working on simulating protein interactions with polymer surface for
tissue engineering applications.

I have developed a primitive model of polymer surface of polystyrene using
"genconf". I have obtained .gro and .itp files using prodrg. But now I
face  error when I use grompp though I included the .itp in .top file! It
says "atomtype CR61 is not found". Now I'm struck at this point from many
days.

Is it that I should add atom types to the ffG43a1nb.itp and ffG43a1bon.itp ?
But then where should I get different parameters.

Thank you for your help.

Harshith Asuri,
3rd year UG student
IIT Kanpur,
http://home.iitk.ac.in/~harshith
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Re: [gmx-users] mdrun producing 0 steps, 0 ps

[Tsjerk Wassenaar]

Hi Travis,

It looks like grompp doesn't parse your .mdp file properly. You should
get an mdout.mdp which contains the parameters as they ended up in
your .tpr file. Check these against your .mdp file. Alternatively you
can 'gmxdump' your .tpr file to check the parameters. Was the .mdp
file originating from a windows machine and are you now under linux
(vv)? Then dos2unix will probably do the trick.

Hope it helps,

Tsjerk

On Tue, Jul 1, 2008 at 12:26 AM, Travis Craddock
<[EMAIL PROTECTED]> wrote:
> Hello,
>
> I'm trying to perform an energy minimization on a Tubulin-GTP-GDP complex in
> a water solvent with sodium ions.  I use the following command to setup up
> the minimization,
>
>> grompp -f em.mdp -c tubulin_b4em.gro -p tubulin3.top -o tubulin_em.tpr
>
> My energy minimization file em*.mdp is:
>
> title   = Tubulin
> cpp = cpp ; location of cpp
> define  = -DFLEX_SPC ; Use Ferguson's Flexible water
> model [4]
> constraints = none
> integrator  = steep
> dt  = 0.002; ps !
> nsteps  = 500
> nstlist = 10
> ns_type = grid
> rlist   = 0.9
> coulombtype = PME ; Use particle-mesh ewald
> rcoulomb= 0.9
> rvdw= 1.0
> fourierspacing  = 0.12
> fourier_nx  = 0
> fourier_ny  = 0
> fourier_nz  = 0
> pme_order   = 4
> ewald_rtol  = 1e-5
> optimize_fft= yes
> ;
> ;   Energy minimizing stuff
> ;
> emtol   = 1000.0
> emstep  = 0.01
>
> When I try and run the energy minimization with the following command,
>
>> mdrun -s tubulin_em.tpr -o tubulin_em.trr -c tubulin_b4pr.gro -g em.log -e
> em.edr
>
> I get the following output (after the initial option list),
>
>
>
> Back Off! I just backed up em.log to ./#em.log.2#
> Reading file tubulin_em.tpr, VERSION 3.3.2 (single precision)
>
> Back Off! I just backed up em.edr to ./#em.edr.2#
> starting mdrun 'TUBULIN ALPHA CHAIN'
> 0 steps,  0.0 ps.
>
>
> Back Off! I just backed up tubulin_e,.trr to ./#tubulin_e,.trr.1#
> Writing final coordinates.
>
> Back Off! I just backed up tubulin_b4pr.gro to ./#tubulin_b4pr.gro.2#
>
>
>
>M E G A - F L O P S   A C C O U N T I N G
>
>   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
>   T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
>   NF=No Forces
>
>  Computing:M-Number M-Flops  % of Flops
> ---
>  LJ0.444057   14.653881 1.9
>  Coulomb   0.442386   11.944422 1.5
>  Coulomb [W3]  0.0318612.548880 0.3
>  Coulomb + LJ  0.326092   12.391496 1.6
>  Coulomb + LJ [W3] 0.0877347.983794 1.0
>  Coulomb + LJ [W3-W3]  2.154199  527.77875567.2
>  Outer nonbonded loop  0.2344922.344920 0.3
>  1,4 nonbonded interactions0.0155951.403550 0.2
>  NS-Pairs  6.889484  144.67916418.4
>  Reset In Box  0.1066520.959868 0.1
>  Shift-X   0.4264562.558736 0.3
>  CG-CoM0.0377691.095301 0.1
>  Bonds 0.0086220.370746 0.0
>  Angles0.0125682.048584 0.3
>  Propers   0.0045331.038057 0.1
>  Impropers 0.0044030.915824 0.1
>  Virial0.1066791.920222 0.2
>  Update0.1066523.306212 0.4
>  Calc-Ekin 0.2133045.759208 0.7
>  Constraint-V  0.1066520.639912 0.1
>  Constraint-Vir0.2944357.066440 0.9
>  Settle0.098145   31.700835 4.0
> ---
>  Total   785.108807   100.0
> ---
>
>   NODE (s)   Real (s)  (%)
>   Time:  1.130  1.000113.0
>
>
>
>
> When I perform my subsequent position restraint, and MD runs there is no
> simulation to observe.  Am I missing something?  Any help would be
> appreciated.  Thanks.
>
> Travis Craddock
> Department of Physics
> University of Alberta
>
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Re: [gmx-users] Missing H's in NADH topology?

[Tsjerk Wassenaar]

Hi Rui,

In the previous version of the gromos force field, the hydrogens on
these groups would be collapsed to the carbons. In the newer force
fields (53*) they are treated explicitly, but I think NADH has not yet
been reparameterized.

Cheers,

Tsjerk

On Mon, Jun 30, 2008 at 9:14 PM, Joaquim Rui Rodrigues
<[EMAIL PROTECTED]> wrote:
> Dear all,
>
> In the .rtp files for the gromos96 forcefield (G43a1, G43a2, G43b1, G45a3, 
> G53a5 and
> G53a6), the aromatic hydrogens that should be bonded to the adenine and 
> nicotinamide
> moieties are missing in NADH. Why is that so? Shouldn't these hydrogens be 
> explicit?
>
> On the other hand, if I generate a topology with prodrg beta, the aromatic 
> hydrogens are
> added as I would expect...
>
> Many thanks,
> Rui Rodrigues
>
> --
> Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] yet another question about PBC...

[Tsjerk Wassenaar]

Hi,

use trjconv

Well, that's just to start the mail with it in stead of ending. g_rms
(g_gyrate, g_rmsf, g_covar) are rather dumb programs, taking a
structure, fitting it to a reference orientation and doing some stuff
on it. They don't check for jumps over the PBC. PBC and fitting don't
go too well together (check some other posts of mine about trjconv,
fitting and pbc in the FML). It's best to do that automatically using
trjconv when your run has finished.

As for the warning, Justin is completely right, but I might add
explicitly that that warning has nothing to do with jumping subunits.

Hope it helps,

Tsjerk

On Mon, Jun 30, 2008 at 5:26 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>
> Ramon Crehuet wrote:
>>
>> Hi,
>> Please don't flame me for asking yet another question about the "out of
>> the box" and PBC issue. I've tried to RTFM, RTFML, but could not find
>> the question I'm asking.
>> I (think) I understand what PBC implies and the fact that "out of the
>> box" makes no sense because the system is periodic and gromacs treats
>> the periodicity correctly. However, when calculating the rmsd of a
>> trajectory with g_rms with respect to the protein I get a warning:
>> "cannot make broken molecules whole without a run input file, don't
>> worry mdrun doesn't write broken molecules".
>> and the rmsd has unrealistic jumps when the chains of the protein (a
>> tetramer) leave the box (but if I calculate distances with g_bond, they
>> are always ok)
>> If I correct the trajectory with trjconf -pbc nojump, the new trajectory
>> seems to behave as expected.
>> So my questions are, i)should I worry about the warning? ii) why does
>> g_rms not treat PBC as expected? Should I use some options?
>>
>
> As far as the warning, it's due to the fact that you specified something
> like a .pdb or .gro file for the -s flag, and not the .tpr file.  Not so
> important in this case, but it would affect, for example, making molecules
> whole with trjconv.
>
> As for the second part, perhaps someone else has better insight, but usually
> the quick answer is to compensate for PBC using trjconv, as you have.  I
> know there are a few messages about this in the list archives, but I think
> they usually end with "use trjconv."
>
> -Justin
>
>
>> Thanks in advance,
>> Ramon
>>
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>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] force field

[hhhh huan]

Dear all gmx users and developers,

I am running a simulation of esters. However,i failed to allocate the force 
field of 1 of the Carbons. (I am using OPLS-AA force field)

-C-C=C-C-C=C-C-
   *

The Carbon atom labeled with symbol * cannot be identified. I checked the 
ffoplsaa.atp file but I cant find the suitable one.

I wish that someone can help me to solve the problems.
Any suggestions and helps are appreciated.

Thanks


  
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[gmx-users] mdrun producing 0 steps, 0 ps

[Travis Craddock]

Hello,

I'm trying to perform an energy minimization on a Tubulin-GTP-GDP complex in 
a water solvent with sodium ions.  I use the following command to setup up 
the minimization,

> grompp -f em.mdp -c tubulin_b4em.gro -p tubulin3.top -o tubulin_em.tpr

My energy minimization file em*.mdp is:

title   = Tubulin 
cpp = cpp ; location of cpp  
define  = -DFLEX_SPC ; Use Ferguson's Flexible water 
model [4] 
constraints = none 
integrator  = steep 
dt  = 0.002; ps ! 
nsteps  = 500 
nstlist = 10  
ns_type = grid 
rlist   = 0.9 
coulombtype = PME ; Use particle-mesh ewald  
rcoulomb= 0.9 
rvdw= 1.0 
fourierspacing  = 0.12 
fourier_nx  = 0 
fourier_ny  = 0 
fourier_nz  = 0 
pme_order   = 4 
ewald_rtol  = 1e-5
optimize_fft= yes 
; 
;   Energy minimizing stuff 
; 
emtol   = 1000.0 
emstep  = 0.01 

When I try and run the energy minimization with the following command,

> mdrun -s tubulin_em.tpr -o tubulin_em.trr -c tubulin_b4pr.gro -g em.log -e 
em.edr 

I get the following output (after the initial option list),



Back Off! I just backed up em.log to ./#em.log.2#
Reading file tubulin_em.tpr, VERSION 3.3.2 (single precision)

Back Off! I just backed up em.edr to ./#em.edr.2#
starting mdrun 'TUBULIN ALPHA CHAIN'
0 steps,  0.0 ps.


Back Off! I just backed up tubulin_e,.trr to ./#tubulin_e,.trr.1#
Writing final coordinates.

Back Off! I just backed up tubulin_b4pr.gro to ./#tubulin_b4pr.gro.2#



M E G A - F L O P S   A C C O U N T I N G

   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
   T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
   NF=No Forces

 Computing:M-Number M-Flops  % of Flops
---
 LJ0.444057   14.653881 1.9
 Coulomb   0.442386   11.944422 1.5
 Coulomb [W3]  0.0318612.548880 0.3
 Coulomb + LJ  0.326092   12.391496 1.6
 Coulomb + LJ [W3] 0.0877347.983794 1.0
 Coulomb + LJ [W3-W3]  2.154199  527.77875567.2
 Outer nonbonded loop  0.2344922.344920 0.3
 1,4 nonbonded interactions0.0155951.403550 0.2
 NS-Pairs  6.889484  144.67916418.4
 Reset In Box  0.1066520.959868 0.1
 Shift-X   0.4264562.558736 0.3
 CG-CoM0.0377691.095301 0.1
 Bonds 0.0086220.370746 0.0
 Angles0.0125682.048584 0.3
 Propers   0.0045331.038057 0.1
 Impropers 0.0044030.915824 0.1
 Virial0.1066791.920222 0.2
 Update0.1066523.306212 0.4
 Calc-Ekin 0.2133045.759208 0.7
 Constraint-V  0.1066520.639912 0.1
 Constraint-Vir0.2944357.066440 0.9
 Settle0.098145   31.700835 4.0
---
 Total   785.108807   100.0
---

   NODE (s)   Real (s)  (%)
   Time:  1.130  1.000113.0




When I perform my subsequent position restraint, and MD runs there is no 
simulation to observe.  Am I missing something?  Any help would be 
appreciated.  Thanks.

Travis Craddock
Department of Physics 
University of Alberta

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Re: [gmx-users] How to calculate dihedral angle ??

[Justin A. Lemkul]

Chih-Ying Lin wrote:


HI
g_chi is designed to help user to calculate the dihedral angles.

I have an organic compound and as the manual describes that .gro ,  
.trr  and ssdump.dat are the required input files to compute and 
collect the dihedral angles with time.




g_chi is for use with the peptide backbone, according to the 
documentation, so I don't know how applicable it necessarily is to your 
situation.


You might be better off using g_angle with an appropriate index group 
for the dihedral(s) of interest.  I have had success using it with small 
organic molecules.


-Justin



For my case, .gro and .trr files are ready.
How to prepare for ssdump.dat?


Also, how do i tell gromacs the calculate the specific dihedral angles 
with time for me??

I did not fully understand the manual's description.

thank you

Lin




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--


Justin A. Lemkul
Graduate Research Assistant
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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AW: [gmx-users] How to calculate dihedral angle ??

[serdar durdagi]

You can use vmd for dihedral angle vs time plots. Download *.gro and *.xtc 
files and use label option in vmd for dihedral angles.
 
serdar


--- Chih-Ying Lin <[EMAIL PROTECTED]> schrieb am Mo, 30.6.2008:

Von: Chih-Ying Lin <[EMAIL PROTECTED]>
Betreff: [gmx-users] How to calculate dihedral angle ??
An: gmx-users@gromacs.org
Datum: Montag, 30. Juni 2008, 19:32



HI
g_chi is designed to help user to calculate the dihedral angles.

I have an organic compound and as the manual describes that .gro ,  .trr  and 
ssdump.dat are the required input files to compute and collect the dihedral 
angles with time.


For my case, .gro and .trr files are ready. 
How to prepare for ssdump.dat?


Also, how do i tell gromacs the calculate the specific dihedral angles with 
time for me??
I did not fully understand the manual's description.

thank you

Lin


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[gmx-users] Missing H's in NADH topology?

[Joaquim Rui Rodrigues]

Dear all,

In the .rtp files for the gromos96 forcefield (G43a1, G43a2, G43b1, G45a3, 
G53a5 and
G53a6), the aromatic hydrogens that should be bonded to the adenine and 
nicotinamide
moieties are missing in NADH. Why is that so? Shouldn't these hydrogens be 
explicit?

On the other hand, if I generate a topology with prodrg beta, the aromatic 
hydrogens are
added as I would expect...

Many thanks,
Rui Rodrigues

--
Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)

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Re: [gmx-users] Uncharged Lysine Charges on Hydrogens from NH2 group 0.36??

[Joseph Schwartz]

This is a link to a table for the OPLS parameters showing the 0.35 for the 
Hydrogens in the RNH2  group (not RCH2NH2--my mistake). It is Table 2 on page 
64. Again, my question is why Gromacs  uses 0.36 for the hydrogens in the non 
n-terminus NH2 group of the uncharged lysine molecule when the published value 
shows 0.35??

zarbi.chem.yale.edu/doc/boss46.pdf 

--- On Sat, 6/28/08, Joseph Schwartz <[EMAIL PROTECTED]> wrote:
From: Joseph Schwartz <[EMAIL PROTECTED]>
Subject: [gmx-users] Uncharged Lysine Charges on Hydrogens from NH2 group 0.36??
To: gmx-users@gromacs.org
Date: Saturday, June 28, 2008, 11:36 AM

I
was wondering why the Hydrogens from the non N-terminus NH2 group in
the uncharged Lysine molecule had charges of 0.36 as specified by
gromacs(H1 and H2) when the Jorgensen published value for H's in
RCH2NH2 was 0.35.  All of the other charges in this molecule I have
found in publications except for those.  The overall charge of the
molecule is 0.02 and if the H's were changed to 0.35 it would make the
overall molecule uncharged.  Would this alteration be valid?

This is part of the topol.top file.


[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB    
chargeB  massB
 1  
 opls_900  1   LYSH  N  1   -0.9    14.0067   ; qtot -0.9
 2   opls_909  1   LYSH H1  1   0.36  1.008   ; qtot 
-0.54
 3   opls_909  1   LYSH H2  1   0.36  1.008   ; qtot 
-0.18
 4   opls_283  1   LYSH CA  1   0.04
 12.011   ; qtot -0.14
 5   opls_140  1   LYSH HA  1   0.06  1.008   ; qtot 
-0.08
 6   opls_136  1   LYSH CB  2  -0.12 12.011   ; qtot 
-0.2
 7   opls_140  1   LYSH    HB1  2   0.06  1.008   ; qtot 
-0.14
 8   opls_140  1   LYSH    HB2 
 2   0.06  1.008   ; qtot -0.08
 9   opls_136  1   LYSH CG  3  -0.12 12.011   ; qtot 
-0.2
    10   opls_140  1   LYSH    HG1  3   0.06  1.008   ; qtot 
-0.14
    11   opls_140  1   LYSH    HG2  3   0.06  1.008   ; qtot 
-0.08
    12   opls_136  1  
 LYSH CD  4  -0.12 12.011   ; qtot -0.2
    13   opls_140  1   LYSH    HD1  4   0.06  1.008   ; qtot 
-0.14
    14   opls_140  1   LYSH    HD2  4   0.06  1.008   ; qtot 
-0.08
    15   opls_292  1   LYSH CE  5   0.19 12.011   ; qtot 
0.11
    16  
 opls_140  1   LYSH    HE1  5   0.06  1.008   ; qtot 0.17
    17   opls_140  1   LYSH    HE2  5   0.06  1.008   ; qtot 
0.23
    18   opls_287  1   LYSH NZ  6   -0.3    14.0067   ; qtot 
-0.07
    19   opls_290  1   LYSH    HZ1  6   0.33  1.008   ; qtot
 0.26
    20   opls_290  1   LYSH    HZ2  6   0.33  1.008   ; qtot 
0.59
    21   opls_290  1   LYSH    HZ3  6   0.33  1.008   ; qtot 
0.92
    22   opls_271  1   LYSH  C  7    0.7 12.011   ; qtot 
1.62
    23   opls_272  1   LYSH O1  7  
 -0.8    15.9994   ; qtot 0.82
    24   opls_272  1   LYSH O2  7   -0.8    15.9994   ; qtot 
0.02





  ___
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--- On Sat, 6/28/08, Joseph Schwartz <[EMAIL PROTECTED]> wrote:
From: Joseph Schwartz <[EMAIL PROTECTED]>
Subject: [gmx-users] Uncharged Lysine Charges on Hydrogens from NH2 group 0.36??
To: gmx-users@gromacs.org
Date: Saturday, June 28, 2008, 11:36 AM

I was wondering why the Hydrogens from the non N-terminus NH2 group in the 
uncharged Lysine molecule had charges of 0.36 as specified by gromacs(H1 and 
H2) when the Jorgensen published value for H's in RCH2NH2 was 0.35.  All of the 
other charges in this molecule I have found in publications except for those.  
The overall charge of the molecule is 0.02 and if the H's were changed to 0.35 
it would make the overall molecule uncharged.  Would this alteration be valid?

This is part of the topol.top file.


[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB    
chargeB  massB
 1  
 opls_900  1   LYSH  N  1   -0.9    14.0067   ; qtot -0.9
 2   opls_909  1   LYSH H1  1   0.36  1.008   ; qtot 
-0.54
 3   opls_909  1   LYSH H2  1   0.36  1.008   ; qtot 
-0.18
 4   opls_283  1   LYSH CA  1   0.04
 12.011   ; qtot -0.14
 5   opls_140  1   LYSH HA  1   0.06  1.008   ; qtot 
-0.08
 6   opls_136  1   LYSH CB  2  -0.12 

[gmx-users] How to calculate dihedral angle ??

[Chih-Ying Lin]

HI
g_chi is designed to help user to calculate the dihedral angles.

I have an organic compound and as the manual describes that .gro ,  .trr
and ssdump.dat are the required input files to compute and collect the
dihedral angles with time.


For my case, .gro and .trr files are ready.
How to prepare for ssdump.dat?


Also, how do i tell gromacs the calculate the specific dihedral angles with
time for me??
I did not fully understand the manual's description.

thank you

Lin
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Re: [gmx-users] Re: warning mesgs

[rams rams]

is that fine if i change the SOL number in the top file created at the first
step ?



On Mon, Jun 30, 2008 at 1:50 PM, rams rams <[EMAIL PROTECTED]> wrote:

> Here's where your problem is.  This step is unnecessary!  Once you have the
> topology, there is no need to re-process with pdb2gmx.  Once you have added
> solvent and ions, simply make the changes to your topology with a text
> editor.
>
> Could you explain what changes I should make in the topology file ??
>
>
>
>
> On Mon, Jun 30, 2008 at 1:44 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>>
>>
>> rams rams wrote:
>>
>>> Dear Justin,
>>>
>>> I am absolutely sorry for the discomfort. Since this is the first time I
>>> am using Gromacs, so things are not clear to me so I am trying things very
>>> randomly thats why I could not keep update the things. Here I restarted
>>> every thing and have a look at and let me know your suggestions:
>>>
>>> pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb –ter –merge
>>>
>>> (since I removed all the hydrogens in my starting insu.pdb so didnt used
>>> -ignh here)
>>>
>>
>> Well, assuming you have all the correct hydrogens in the right place,
>> that's fine, but in general, it is very easy to let pdb2gmx do the work for
>> you and use -ignh.  If it generated the topology for you, then that's fine.
>>
>>  editconf -f insu_p.pdb -o insu_pb.pdb -box 6.0 6.0 6.0 -center 3.0 3.0
>>> 3.0
>>>
>>> genbox -cp insu_pb.pdb -cs spc216.gro -o insu_pw.pdb -p insu_p.top
>>>
>>> grompp -f eminimization.mdp -c  insu_pw.pdb -p insu_p.top -o MM_insu.tp
>>>
>>> genion -s MM_insu.tpr -o insu_pwi.pdb -conc 0.008 –neutral
>>>
>>> pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.pdb -inter –merge
>>> -ignh
>>>
>>>
>> Here's where your problem is.  This step is unnecessary!  Once you have
>> the topology, there is no need to re-process with pdb2gmx.  Once you have
>> added solvent and ions, simply make the changes to your topology with a text
>> editor.
>>
>>  grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o
>>> MM_insu.tpr
>>>
>>>
>>>
>> It has already been correctly pointed out by another user that you
>> specified -o .pdb in the above step, but then called for the .gro equivalent
>> here.  That would be a problem.
>>
>> Basically, once the genion step is done, and you have made the appropriate
>> changes to the topology (which can also be done with the -p flag of genion),
>> then proceed to grompp.
>>
>> This makes much more sense, and it is easier to get help when it is
>> clearly presented like this!
>>
>> -Justin
>>
>>
>>> The following is the error:
>>>
>>>
>>>
>>>
>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
>>> checking input for internal consistency...
>>> calling /lib/cpp...
>>> processing topology...
>>> Generated 716 of the 2628 non-bonded parameter combinations
>>> Generating 1-4 interactions: fudge = 1
>>> Generated 1046 of the 2628 1-4 parameter combinations
>>> Excluding 3 bonded neighbours for Protein 1
>>> turning all bonds into constraints...
>>> Excluding 2 bonded neighbours for SOL 6878
>>> turning all bonds into constraints...
>>> NOTE:
>>>  System has non-zero total charge: -2.00e+00
>>>
>>> processing coordinates...
>>> ---
>>> Program grompp, VERSION 3.3.1
>>> Source code file: futil.c, line: 340
>>>
>>> File input/output error:
>>> insu_pwi2MM.gro
>>>
>>>
>>> Ram.
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Jun 30, 2008 at 6:45 AM, Justin A. Lemkul <[EMAIL PROTECTED]>> [EMAIL PROTECTED]>> wrote:
>>>
>>>It would be helpful if all of this was on one thread, with replies
>>>embedded.  I have sent several replies to your questions, all of
>>>which have gone unacknowledged.  It makes it very difficult for
>>>anyone (myself or someone else) to give advice if we don't know
>>>what you're doing or what you've tried.  Even if something didn't
>>>work based on what I, or anyone else, tells you, it is nice to
>>>know that "I tried this, but I still have a problem, which is
>>>shown here: (exact error/warning/problem)."
>>>
>>>As I've said before, exact procedural details of what you've done
>>>are essential for sorting out strange problems like this.  This
>>>means - *exact* (copy and paste) command lines from pdb2gmx, and
>>>any error messages you receive.  Also, any manipulations you have
>>>made to your input .pdb file.  It seems to me that you've probably
>>>edited your file to have only one chain identifier, and hence why
>>>pdb2gmx is trying to make everything one molecule.
>>>
>>>The -merge option of pdb2gmx is what you want (see pdb2gmx -h).
>>> If the following command line doesn't work, it would be nice to
>>>see an exact reason (i.e., copy/paste from the
>>>error/warning/whatever):
>>>
>>>pdb2gmx -f (input).pdb -ignh -ter -merge
>>>
>>>I got the above to work perfectly on an insulin structure I found
>>>in the RCSB (1ZNI), after deleting chain

Re: [gmx-users] Re: warning mesgs

[rams rams]

Hi,

I mistyped the command as you mentioned. I did used the following:

grompp -f eminimization.mdp -c insu_pwi2MM.pdb -p insu_pwi.top -o
MM_insu.tpr

Now the error is the following:
turning all bonds into constraints...
NOTE:
  System has non-zero total charge: -2.00e+00

processing coordinates...
---
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (insu_pwi2MM.pdb, 21149)
 does not match topology (insu_pwi.top, 21157)

Ram.


On Mon, Jun 30, 2008 at 12:45 PM, Nuno Azoia <[EMAIL PROTECTED]> wrote:

> Hi!
>
> I'm new to Gromacs, so maybe my answer is not 100% correct, but it seems to
> me that you forgot to create the required insu_pwi2MM.gro file. In your last
> pdb2gmx command you just created insu_pwi2MM.pdb, and then the last grompp
> command cannot found the insu_pwi2MM.gro file. I think you have to repeat
> the last pdb2gmx command in order to create the .gro file, something like
>
> pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.*gro* -inter –merge
> -ignh
>
> (the same command you have written but with different output file)
>
> Nuno Azoia
>
> rams rams wrote:
>
>> Dear Justin,
>>
>> I am absolutely sorry for the discomfort. Since this is the first time I
>> am using Gromacs, so things are not clear to me so I am trying things very
>> randomly thats why I could not keep update the things. Here I restarted
>> every thing and have a look at and let me know your suggestions:
>>
>> pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb –ter –merge
>>
>> (since I removed all the hydrogens in my starting insu.pdb so didnt used
>> -ignh here)
>>
>> editconf -f insu_p.pdb -o insu_pb.pdb -box 6.0 6.0 6.0 -center 3.0 3.0 3.0
>>
>> genbox -cp insu_pb.pdb -cs spc216.gro -o insu_pw.pdb -p insu_p.top
>>
>> grompp -f eminimization.mdp -c  insu_pw.pdb -p insu_p.top -o MM_insu.tp
>>
>> genion -s MM_insu.tpr -o insu_pwi.pdb -conc 0.008 –neutral
>>
>> pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.pdb -inter –merge
>> -ignh
>>
>> grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o
>> MM_insu.tpr
>>
>>
>>
>> The following is the error:
>>
>>
>>
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
>> checking input for internal consistency...
>> calling /lib/cpp...
>> processing topology...
>> Generated 716 of the 2628 non-bonded parameter combinations
>> Generating 1-4 interactions: fudge = 1
>> Generated 1046 of the 2628 1-4 parameter combinations
>> Excluding 3 bonded neighbours for Protein 1
>> turning all bonds into constraints...
>> Excluding 2 bonded neighbours for SOL 6878
>> turning all bonds into constraints...
>> NOTE:
>>  System has non-zero total charge: -2.00e+00
>>
>> processing coordinates...
>> ---
>> Program grompp, VERSION 3.3.1
>> Source code file: futil.c, line: 340
>>
>> File input/output error:
>> insu_pwi2MM.gro
>>
>>
>> Ram.
>>
>>
>>
>>
>>
>> On Mon, Jun 30, 2008 at 6:45 AM, Justin A. Lemkul <[EMAIL PROTECTED]> [EMAIL PROTECTED]>> wrote:
>>
>>It would be helpful if all of this was on one thread, with replies
>>embedded.  I have sent several replies to your questions, all of
>>which have gone unacknowledged.  It makes it very difficult for
>>anyone (myself or someone else) to give advice if we don't know
>>what you're doing or what you've tried.  Even if something didn't
>>work based on what I, or anyone else, tells you, it is nice to
>>know that "I tried this, but I still have a problem, which is
>>shown here: (exact error/warning/problem)."
>>
>>As I've said before, exact procedural details of what you've done
>>are essential for sorting out strange problems like this.  This
>>means - *exact* (copy and paste) command lines from pdb2gmx, and
>>any error messages you receive.  Also, any manipulations you have
>>made to your input .pdb file.  It seems to me that you've probably
>>edited your file to have only one chain identifier, and hence why
>>pdb2gmx is trying to make everything one molecule.
>>
>>The -merge option of pdb2gmx is what you want (see pdb2gmx -h).
>> If the following command line doesn't work, it would be nice to
>>see an exact reason (i.e., copy/paste from the
>>error/warning/whatever):
>>
>>pdb2gmx -f (input).pdb -ignh -ter -merge
>>
>>I got the above to work perfectly on an insulin structure I found
>>in the RCSB (1ZNI), after deleting chains C and D from the .pdb
>>file.  If your structure continues to give you headaches, try this
>>one to make sure that your Gromacs installation is working
>>properly (something I inquired about several days ago...)
>>
>>-Justin
>>
>>rams rams wrote:
>>
>>HI,
>>
>>When I use the merge command along with pdb2gmx to form inter
>>disulphide bonds between two different chains, its removing

Re: [gmx-users] Re: warning mesgs

[Justin A. Lemkul]

rams rams wrote:

Dear Justin,

I am absolutely sorry for the discomfort. Since this is the first time 
I am using Gromacs, so things are not clear to me so I am trying 
things very randomly thats why I could not keep update the things. 
Here I restarted every thing and have a look at and let me know your 
suggestions:


pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb –ter –merge

(since I removed all the hydrogens in my starting insu.pdb so didnt 
used -ignh here)


Well, assuming you have all the correct hydrogens in the right place, 
that's fine, but in general, it is very easy to let pdb2gmx do the work 
for you and use -ignh.  If it generated the topology for you, then 
that's fine.



editconf -f insu_p.pdb -o insu_pb.pdb -box 6.0 6.0 6.0 -center 3.0 3.0 3.0

genbox -cp insu_pb.pdb -cs spc216.gro -o insu_pw.pdb -p insu_p.top

grompp -f eminimization.mdp -c  insu_pw.pdb -p insu_p.top -o MM_insu.tp

genion -s MM_insu.tpr -o insu_pwi.pdb -conc 0.008 –neutral

pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.pdb -inter 
–merge -ignh




Here's where your problem is.  This step is unnecessary!  Once you have 
the topology, there is no need to re-process with pdb2gmx.  Once you 
have added solvent and ions, simply make the changes to your topology 
with a text editor.


grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o 
MM_insu.tpr





It has already been correctly pointed out by another user that you 
specified -o .pdb in the above step, but then called for the .gro 
equivalent here.  That would be a problem.


Basically, once the genion step is done, and you have made the 
appropriate changes to the topology (which can also be done with the -p 
flag of genion), then proceed to grompp.


This makes much more sense, and it is easier to get help when it is 
clearly presented like this!


-Justin



The following is the error:




Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 716 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1046 of the 2628 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 6878
turning all bonds into constraints...
NOTE:
  System has non-zero total charge: -2.00e+00

processing coordinates...
---
Program grompp, VERSION 3.3.1
Source code file: futil.c, line: 340

File input/output error:
insu_pwi2MM.gro


Ram.





On Mon, Jun 30, 2008 at 6:45 AM, Justin A. Lemkul <[EMAIL PROTECTED] 
> wrote:


It would be helpful if all of this was on one thread, with replies
embedded.  I have sent several replies to your questions, all of
which have gone unacknowledged.  It makes it very difficult for
anyone (myself or someone else) to give advice if we don't know
what you're doing or what you've tried.  Even if something didn't
work based on what I, or anyone else, tells you, it is nice to
know that "I tried this, but I still have a problem, which is
shown here: (exact error/warning/problem)."

As I've said before, exact procedural details of what you've done
are essential for sorting out strange problems like this.  This
means - *exact* (copy and paste) command lines from pdb2gmx, and
any error messages you receive.  Also, any manipulations you have
made to your input .pdb file.  It seems to me that you've probably
edited your file to have only one chain identifier, and hence why
pdb2gmx is trying to make everything one molecule.

The -merge option of pdb2gmx is what you want (see pdb2gmx -h).
 If the following command line doesn't work, it would be nice to
see an exact reason (i.e., copy/paste from the
error/warning/whatever):

pdb2gmx -f (input).pdb -ignh -ter -merge

I got the above to work perfectly on an insulin structure I found
in the RCSB (1ZNI), after deleting chains C and D from the .pdb
file.  If your structure continues to give you headaches, try this
one to make sure that your Gromacs installation is working
properly (something I inquired about several days ago...)

-Justin

rams rams wrote:

HI,

When I use the merge command along with pdb2gmx to form inter
disulphide bonds between two different chains, its removing a
water molecule to connect the two ends. Its like forming a
peptide bond which I dont wish. Is there any way to tell to
gromacs, to create the inter dishulphide bonds without
creating the peptide bond between the two chains ?



On Fri, Jun 27, 2008 at 6:51 PM, rams rams
<[EMAIL PROTECTED] 
>> wrote:

   Hi,

   I have three di sulphide bonds in m

Re: [gmx-users] Re: warning mesgs

[Nuno Azoia]

Hi!

I'm new to Gromacs, so maybe my answer is not 100% correct, but it seems 
to me that you forgot to create the required insu_pwi2MM.gro file. In 
your last pdb2gmx command you just created insu_pwi2MM.pdb, and then the 
last grompp command cannot found the insu_pwi2MM.gro file. I think you 
have to repeat the last pdb2gmx command in order to create the .gro 
file, something like


pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.*gro* -inter 
–merge -ignh


(the same command you have written but with different output file)

Nuno Azoia

rams rams wrote:

Dear Justin,

I am absolutely sorry for the discomfort. Since this is the first time 
I am using Gromacs, so things are not clear to me so I am trying 
things very randomly thats why I could not keep update the things. 
Here I restarted every thing and have a look at and let me know your 
suggestions:


pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb –ter –merge

(since I removed all the hydrogens in my starting insu.pdb so didnt 
used -ignh here)


editconf -f insu_p.pdb -o insu_pb.pdb -box 6.0 6.0 6.0 -center 3.0 3.0 3.0

genbox -cp insu_pb.pdb -cs spc216.gro -o insu_pw.pdb -p insu_p.top

grompp -f eminimization.mdp -c  insu_pw.pdb -p insu_p.top -o MM_insu.tp

genion -s MM_insu.tpr -o insu_pwi.pdb -conc 0.008 –neutral

pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.pdb -inter 
–merge -ignh


grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o 
MM_insu.tpr




The following is the error:




Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 716 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1046 of the 2628 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 6878
turning all bonds into constraints...
NOTE:
  System has non-zero total charge: -2.00e+00

processing coordinates...
---
Program grompp, VERSION 3.3.1
Source code file: futil.c, line: 340

File input/output error:
insu_pwi2MM.gro


Ram.





On Mon, Jun 30, 2008 at 6:45 AM, Justin A. Lemkul <[EMAIL PROTECTED] 
> wrote:


It would be helpful if all of this was on one thread, with replies
embedded.  I have sent several replies to your questions, all of
which have gone unacknowledged.  It makes it very difficult for
anyone (myself or someone else) to give advice if we don't know
what you're doing or what you've tried.  Even if something didn't
work based on what I, or anyone else, tells you, it is nice to
know that "I tried this, but I still have a problem, which is
shown here: (exact error/warning/problem)."

As I've said before, exact procedural details of what you've done
are essential for sorting out strange problems like this.  This
means - *exact* (copy and paste) command lines from pdb2gmx, and
any error messages you receive.  Also, any manipulations you have
made to your input .pdb file.  It seems to me that you've probably
edited your file to have only one chain identifier, and hence why
pdb2gmx is trying to make everything one molecule.

The -merge option of pdb2gmx is what you want (see pdb2gmx -h).
 If the following command line doesn't work, it would be nice to
see an exact reason (i.e., copy/paste from the
error/warning/whatever):

pdb2gmx -f (input).pdb -ignh -ter -merge

I got the above to work perfectly on an insulin structure I found
in the RCSB (1ZNI), after deleting chains C and D from the .pdb
file.  If your structure continues to give you headaches, try this
one to make sure that your Gromacs installation is working
properly (something I inquired about several days ago...)

-Justin

rams rams wrote:

HI,

When I use the merge command along with pdb2gmx to form inter
disulphide bonds between two different chains, its removing a
water molecule to connect the two ends. Its like forming a
peptide bond which I dont wish. Is there any way to tell to
gromacs, to create the inter dishulphide bonds without
creating the peptide bond between the two chains ?



On Fri, Jun 27, 2008 at 6:51 PM, rams rams
<[EMAIL PROTECTED] 
>> wrote:

   Hi,

   I have three di sulphide bonds in my crystal structure. In the
   topology file it left blanks at the corresponding sulphur
   connectivities (i.e., values corresponding to gb_, ga_. gd_ ).
   When I try to create the .tpr file it complains the following:

   processing topology...
   Generated 716 of the 2628 non-bonded parameter combinations
   Generating 1-4 interaction

Re: [gmx-users] Re: warning mesgs

[rams rams]

Dear Justin,

I am absolutely sorry for the discomfort. Since this is the first time I am
using Gromacs, so things are not clear to me so I am trying things very
randomly thats why I could not keep update the things. Here I restarted
every thing and have a look at and let me know your suggestions:

pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb –ter –merge
(since I removed all the hydrogens in my starting insu.pdb so didnt used
-ignh here)

editconf -f insu_p.pdb -o insu_pb.pdb -box 6.0 6.0 6.0 -center 3.0 3.0 3.0

genbox -cp insu_pb.pdb -cs spc216.gro -o insu_pw.pdb -p insu_p.top

grompp -f eminimization.mdp -c  insu_pw.pdb -p insu_p.top -o MM_insu.tp

genion -s MM_insu.tpr -o insu_pwi.pdb -conc 0.008 –neutral

pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.pdb -inter –merge
-ignh

grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o
MM_insu.tpr


The following is the error:



Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 716 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1046 of the 2628 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 6878
turning all bonds into constraints...
NOTE:
  System has non-zero total charge: -2.00e+00

processing coordinates...
---
Program grompp, VERSION 3.3.1
Source code file: futil.c, line: 340

File input/output error:
insu_pwi2MM.gro


Ram.





On Mon, Jun 30, 2008 at 6:45 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

> It would be helpful if all of this was on one thread, with replies
> embedded.  I have sent several replies to your questions, all of which have
> gone unacknowledged.  It makes it very difficult for anyone (myself or
> someone else) to give advice if we don't know what you're doing or what
> you've tried.  Even if something didn't work based on what I, or anyone
> else, tells you, it is nice to know that "I tried this, but I still have a
> problem, which is shown here: (exact error/warning/problem)."
>
> As I've said before, exact procedural details of what you've done are
> essential for sorting out strange problems like this.  This means - *exact*
> (copy and paste) command lines from pdb2gmx, and any error messages you
> receive.  Also, any manipulations you have made to your input .pdb file.  It
> seems to me that you've probably edited your file to have only one chain
> identifier, and hence why pdb2gmx is trying to make everything one molecule.
>
> The -merge option of pdb2gmx is what you want (see pdb2gmx -h).  If the
> following command line doesn't work, it would be nice to see an exact reason
> (i.e., copy/paste from the error/warning/whatever):
>
> pdb2gmx -f (input).pdb -ignh -ter -merge
>
> I got the above to work perfectly on an insulin structure I found in the
> RCSB (1ZNI), after deleting chains C and D from the .pdb file.  If your
> structure continues to give you headaches, try this one to make sure that
> your Gromacs installation is working properly (something I inquired about
> several days ago...)
>
> -Justin
>
> rams rams wrote:
>
>> HI,
>>
>> When I use the merge command along with pdb2gmx to form inter disulphide
>> bonds between two different chains, its removing a water molecule to connect
>> the two ends. Its like forming a peptide bond which I dont wish. Is there
>> any way to tell to gromacs, to create the inter dishulphide bonds without
>> creating the peptide bond between the two chains ?
>>
>>
>>
>> On Fri, Jun 27, 2008 at 6:51 PM, rams rams <[EMAIL PROTECTED] > [EMAIL PROTECTED]>> wrote:
>>
>>Hi,
>>
>>I have three di sulphide bonds in my crystal structure. In the
>>topology file it left blanks at the corresponding sulphur
>>connectivities (i.e., values corresponding to gb_, ga_. gd_ ).
>>When I try to create the .tpr file it complains the following:
>>
>>processing topology...
>>Generated 716 of the 2628 non-bonded parameter combinations
>>Generating 1-4 interactions: fudge = 1
>>Generated 1046 of the 2628 1-4 parameter combinations
>>WARNING 1 [file "insu_pwi.top", line 607]:
>>  No default G96Bond types, using zeroes
>>WARNING 2 [file "insu_pwi.top", line 745]:
>>  No default G96Bond types, using zeroes
>>WARNING 3 [file "insu_pwi.top", line 2008]:
>>  No default G96Angle types, using zeroes
>>WARNING 4 [file "insu_pwi.top", line 2209]:
>>  No default G96Angle types, using zeroes
>>WARNING 5 [file "insu_pwi.top", line 2345]:
>>  No default G96Angle types, using zeroes
>>WARNING 6 [file "insu_pwi.top", line 2512]:
>>  No default G96Angle types, using zeroes
>>WARNING 7 [file "insu_pwi.top", line 2748]:
>>  No default Proper Dih. types, using zeroes
>>WARNING 8 [file "insu_pwi.top", line 2820]:
>>  

Re: [gmx-users] Segmentation fault with gromacs 3.3.3

[Cesar Avila]

Once again, in reply to myself I could state that gromacs-3.3.3 won't
build correctly on debian systems with gcc-4.3 neither. gmxtest simple
dumps the following information.

*** glibc detected *** mdrun: realloc(): invalid next size: 0x082a20d0 ***
=== Backtrace: =
/lib/i686/cmov/libc.so.6[0xb7c0a673]
/lib/i686/cmov/libc.so.6(realloc+0x10b)[0xb7c0c5cb]
mdrun[0x8146fdd]
=== Memory map: 
08048000-08283000 r-xp  08:05 1182361/usr/local/gromacs/bin/mdrun
08283000-0828a000 rwxp 0023b000 08:05 1182361/usr/local/gromacs/bin/mdrun
0828a000-082b rwxp 0828a000 00:00 0  [heap]
b7a0-b7a21000 rwxp b7a0 00:00 0
b7a21000-b7b0 ---p b7a21000 00:00 0
b7b5c000-b7b5e000 rwxp b7b5c000 00:00 0
b7b5e000-b7b62000 r-xp  08:05 654102 /usr/lib/libXdmcp.so.6.0.0
b7b62000-b7b63000 rwxp 3000 08:05 654102 /usr/lib/libXdmcp.so.6.0.0
b7b63000-b7b65000 r-xp  08:05 656196 /usr/lib/libXau.so.6.0.0
b7b65000-b7b66000 rwxp 1000 08:05 656196 /usr/lib/libXau.so.6.0.0
b7b66000-b7b68000 r-xp  08:05 963745 /lib/i686/cmov/libdl-2.7.so
b7b68000-b7b6a000 rwxp 1000 08:05 963745 /lib/i686/cmov/libdl-2.7.so
b7b6a000-b7b81000 r-xp  08:05 653184 /usr/lib/libxcb.so.1.0.0
b7b81000-b7b82000 rwxp 00016000 08:05 653184 /usr/lib/libxcb.so.1.0.0
b7b82000-b7b83000 r-xp  08:05 653441
/usr/lib/libxcb-xlib.so.0.0.0
b7b83000-b7b84000 rwxp  08:05 653441
/usr/lib/libxcb-xlib.so.0.0.0
b7b84000-b7b85000 rwxp b7b84000 00:00 0
b7b85000-b7b99000 r-xp  08:05 963756
/lib/i686/cmov/libpthread-2.7.so
b7b99000-b7b9b000 rwxp 00013000 08:05 963756
/lib/i686/cmov/libpthread-2.7.so
b7b9b000-b7b9d000 rwxp b7b9b000 00:00 0
b7b9d000-b7ce5000 r-xp  08:05 963742 /lib/i686/cmov/libc-2.7.so
b7ce5000-b7ce6000 r-xp 00148000 08:05 963742 /lib/i686/cmov/libc-2.7.so
b7ce6000-b7ce8000 rwxp 00149000 08:05 963742 /lib/i686/cmov/libc-2.7.so
b7ce8000-b7ceb000 rwxp b7ce8000 00:00 0
b7ceb000-b7dd6000 r-xp  08:05 219962 /usr/lib/libX11.so.6.2.0
b7dd6000-b7dd9000 rwxp 000eb000 08:05 219962 /usr/lib/libX11.so.6.2.0
b7dd9000-b7dda000 rwxp b7dd9000 00:00 0
b7dda000-b7dee000 r-xp  08:05 654098 /usr/lib/libICE.so.6.3.0
b7dee000-b7def000 rwxp 00014000 08:05 654098 /usr/lib/libICE.so.6.3.0
b7def000-b7df1000 rwxp b7def000 00:00 0
b7df1000-b7df8000 r-xp  08:05 656152 /usr/lib/libSM.so.6.0.0
b7df8000-b7df9000 rwxp 6000 08:05 656152 /usr/lib/libSM.so.6.0.0
b7df9000-b7e1c000 r-xp  08:05 963746 /lib/i686/cmov/libm-2.7.so
b7e1c000-b7e1e000 rwxp 00023000 08:05 963746 /lib/i686/cmov/libm-2.7.so
b7e1e000-b7e1f000 rwxp b7e1e000 00:00 0
b7e1f000-b7efc000 r-xp  08:05 652016 /usr/lib/libfftw3f.so.3.1.2
b7efc000-b7f02000 rwxp 000dd000 08:05 652016 /usr/lib/libfftw3f.so.3.1.2
b7f02000-b7f16000 r-xp  08:05 963748 /lib/i686/cmov/libnsl-2.7.so
b7f16000-b7f18000 rwxp 00013000 08:05 963748 /lib/i686/cmov/libnsl-2.7.so
b7f18000-b7f1a000 rwxp b7f18000 00:00 0
b7f1d000-b7f29000 r-xp  08:05 676535 /lib/libgcc_s.so.1
b7f29000-b7f2a000 rwxp b000 08:05 676535 /lib/libgcc_s.so.1
b7f2a000-b7f2d000 rwxp b7f2a000 00:00 0
b7f2d000-b7f47000 r-xp  08:05 677881 /lib/ld-2.7.so
b7f47000-b7f49000 rwxp 00019000 08:05 677881 /lib/ld-2.7.so
bf985000-bf99c000 rwxp bffe9000 00:00 0  [stack]
e000-f000 r-xp  00:00 0  [vdso]
sh: line 1:  6267 Abortadomdrun > mdrun.out 2>&1
FAILED. Check files in rb1
1 out of 16 simple tests FAILED

On the other hand, mpi version of gromacs built on the same system,
succesfully passes all simple test.

Cesar Avila escribió:
> It seems to be a problem related to the debian package. I have compiled
> gromacs 3.3.3 from source with gcc-4.3 and apparently the problem has
> dissapeared. Perhaps, the binaries on the debian package were compiled
> with gcc-4.1.
>
>
> Cesar Avila escribió:
>> Dear all,
>> I am new to the gromacs simulation package. Thus far I have been using
>> Charmm and NAMD, but now I am interested on testing Marrink's
>> Coarse-Grained Martini FF. I managed to setup an initial configuration for
>> a protein in a water box. After a few minimization steps, I ran the
>> simulation for about 10 ns until it crashed with a Segmentation fault
>> message.
>> Using tpbconv, I resumed the simulation from 10200 ps step. Nevertheless I
>> systematically found a segmentation fault  error on step 6530. Using mdrun
>> -nocompact gives no additional information about the crash. When I use
>> mdrun -debug the simulation is able to run without any problem (until I
>> run out of disk space).
>> I found the same error to occur on both a Pentium IV (debian etch) and an
>> Intel Core 2 Duo (Debian lenny). Both systems
>> are running gromacs 3.3.3 from Debian testing packages. If anyone is
>> interested on reproducing the error on their own computer, I can s

Re: [gmx-users] yet another question about PBC...

[Justin A. Lemkul]

Ramon Crehuet wrote:

Hi,
Please don't flame me for asking yet another question about the "out of
the box" and PBC issue. I've tried to RTFM, RTFML, but could not find
the question I'm asking.
I (think) I understand what PBC implies and the fact that "out of the
box" makes no sense because the system is periodic and gromacs treats
the periodicity correctly. However, when calculating the rmsd of a
trajectory with g_rms with respect to the protein I get a warning:
"cannot make broken molecules whole without a run input file, don't
worry mdrun doesn't write broken molecules".
and the rmsd has unrealistic jumps when the chains of the protein (a
tetramer) leave the box (but if I calculate distances with g_bond, they
are always ok)
If I correct the trajectory with trjconf -pbc nojump, the new trajectory
seems to behave as expected.
So my questions are, i)should I worry about the warning? ii) why does
g_rms not treat PBC as expected? Should I use some options?
  


As far as the warning, it's due to the fact that you specified something 
like a .pdb or .gro file for the -s flag, and not the .tpr file.  Not so 
important in this case, but it would affect, for example, making 
molecules whole with trjconv.


As for the second part, perhaps someone else has better insight, but 
usually the quick answer is to compensate for PBC using trjconv, as you 
have.  I know there are a few messages about this in the list archives, 
but I think they usually end with "use trjconv."


-Justin



Thanks in advance,
Ramon

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--


Justin A. Lemkul
Graduate Research Assistant
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] yet another question about PBC...

[Ramon Crehuet]

Hi,
Please don't flame me for asking yet another question about the "out of
the box" and PBC issue. I've tried to RTFM, RTFML, but could not find
the question I'm asking.
I (think) I understand what PBC implies and the fact that "out of the
box" makes no sense because the system is periodic and gromacs treats
the periodicity correctly. However, when calculating the rmsd of a
trajectory with g_rms with respect to the protein I get a warning:
"cannot make broken molecules whole without a run input file, don't
worry mdrun doesn't write broken molecules".
and the rmsd has unrealistic jumps when the chains of the protein (a
tetramer) leave the box (but if I calculate distances with g_bond, they
are always ok)
If I correct the trajectory with trjconf -pbc nojump, the new trajectory
seems to behave as expected.
So my questions are, i)should I worry about the warning? ii) why does
g_rms not treat PBC as expected? Should I use some options?
Thanks in advance,
Ramon

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[gmx-users] typo on manual 3.3 pdf

[Alan]

On gmx_manual-3.3.pdf, page 101, where one reads:

However if you wat to specify N ...



Should be, I guess:

However if you want to specify N y

Cheers,
Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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[gmx-users] FFGMX. Units of a constant.

[Vitaly Chaban]

Hi,

What is the units for dihedral reastaints used in FFGMX?

What confused me:
/usr/share/gromacs/top/ffgmxbon.itp:
CO2 0.000 167.360
C   OM2 0.000 167.360
C   NT2 0.000 167.360

x2top -h:
 -kb   real 40  Bonded force constant (kJ/mol/nm^2)
 -kt   real400  Angle force constant (kJ/mol/rad^2)
(!!!)-kp   real  5  Dihedral angle force constant (kJ/mol/rad^2)


Why so big difference between the default value for x2top and the
usual values listed in ffgmxbon.itp? At the same time, constants for
bonds and angles are very close in both places.


Thanks.

-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svobody sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban

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Re: [gmx-users] Which ensemble for membrane proteins?

[Justin A. Lemkul]

sudheer babu wrote:

Hi everybody,
   I have read one review article( 
dissertations.ub.rug.nl/FILES/faculties/science/1998/d.p.tieleman/c1.pdf 
 
) about membrane proteins tells about POPC alone simulations should 
run in NPT but not in NVT conditions. Regarding protein run in both 
some time NPT remain time NVT, till now fine . But when protein 
inserted into POPC in which ensemble conditions have to follow? Can 
anyone knows please tell me

Thanks in advance.
  


I would continue searching the literature.  In the linked article you 
provide, it is mentioned that NVT can induce artefacts, so that is 
probably a good reason to avoid it for any system containing a lipid 
bilayer.  I have never seen a published membrane protein paper that used 
NVT, although I certainly haven't read them all!


Another good article to read (among many) is:  Kandt, et al. (2007) 
Methods. 41: 475-488.  Anything else by Tieleman and associates is good, 
so starting your search there would be a reasonable choice.


-Justin




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--


Justin A. Lemkul
Graduate Research Assistant
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] g_mindist possible bug - missing a frame

[shayamra]

Dear Gromacs users,
I used g_mindist in order to generate minimum distance between a  
certain protein and a ligand. I invoked -od (to generate xvg) and -o  
(to generate atom-pairs list).
Following that, I aligned the atom-pairs columns next to the distance  
columns so to have a list of [protein index] [ligand index] and  
[distance] for each frame.

Oddly enough I got one frame that had mindist but no corresponding atom-pairs.
I checked the .out file and indeed the list just skips to the next  
frame/atom-pair in the list.

Is there any particular reason this might happen?

Regards,
-Shay



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[gmx-users] Which ensemble for membrane proteins?

[sudheer babu]

Hi everybody,
   I have read one review article(
dissertations.ub.rug.nl/FILES/faculties/science/1998/d.p.tieleman/c1.pdf )
about membrane proteins tells about POPC alone simulations should run in NPT
but not in NVT conditions. Regarding protein run in both some time NPT
remain time NVT, till now fine . But when protein inserted into POPC in
which ensemble conditions have to follow? Can anyone knows please tell me
Thanks in advance.
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Re: [gmx-users] Re: warning mesgs

[Justin A. Lemkul]

It would be helpful if all of this was on one thread, with replies 
embedded.  I have sent several replies to your questions, all of which 
have gone unacknowledged.  It makes it very difficult for anyone (myself 
or someone else) to give advice if we don't know what you're doing or 
what you've tried.  Even if something didn't work based on what I, or 
anyone else, tells you, it is nice to know that "I tried this, but I 
still have a problem, which is shown here: (exact error/warning/problem)."


As I've said before, exact procedural details of what you've done are 
essential for sorting out strange problems like this.  This means - 
*exact* (copy and paste) command lines from pdb2gmx, and any error 
messages you receive.  Also, any manipulations you have made to your 
input .pdb file.  It seems to me that you've probably edited your file 
to have only one chain identifier, and hence why pdb2gmx is trying to 
make everything one molecule.


The -merge option of pdb2gmx is what you want (see pdb2gmx -h).  If the 
following command line doesn't work, it would be nice to see an exact 
reason (i.e., copy/paste from the error/warning/whatever):


pdb2gmx -f (input).pdb -ignh -ter -merge

I got the above to work perfectly on an insulin structure I found in the 
RCSB (1ZNI), after deleting chains C and D from the .pdb file.  If your 
structure continues to give you headaches, try this one to make sure 
that your Gromacs installation is working properly (something I inquired 
about several days ago...)


-Justin

rams rams wrote:

HI,

When I use the merge command along with pdb2gmx to form inter 
disulphide bonds between two different chains, its removing a water 
molecule to connect the two ends. Its like forming a peptide bond 
which I dont wish. Is there any way to tell to gromacs, to create the 
inter dishulphide bonds without creating the peptide bond between the 
two chains ?




On Fri, Jun 27, 2008 at 6:51 PM, rams rams <[EMAIL PROTECTED] 
> wrote:


Hi,

I have three di sulphide bonds in my crystal structure. In the
topology file it left blanks at the corresponding sulphur
connectivities (i.e., values corresponding to gb_, ga_. gd_ ).
When I try to create the .tpr file it complains the following:

processing topology...
Generated 716 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1046 of the 2628 1-4 parameter combinations
WARNING 1 [file "insu_pwi.top", line 607]:
  No default G96Bond types, using zeroes
WARNING 2 [file "insu_pwi.top", line 745]:
  No default G96Bond types, using zeroes
WARNING 3 [file "insu_pwi.top", line 2008]:
  No default G96Angle types, using zeroes
WARNING 4 [file "insu_pwi.top", line 2209]:
  No default G96Angle types, using zeroes
WARNING 5 [file "insu_pwi.top", line 2345]:
  No default G96Angle types, using zeroes
WARNING 6 [file "insu_pwi.top", line 2512]:
  No default G96Angle types, using zeroes
WARNING 7 [file "insu_pwi.top", line 2748]:
  No default Proper Dih. types, using zeroes
WARNING 8 [file "insu_pwi.top", line 2820]:
  No default Proper Dih. types, using zeroes
WARNING 9 [file "insu_pwi.top", line 2863]:
  No default Proper Dih. types, using zeroes
WARNING 10 [file "insu_pwi.top", line 2919]:
  No default Proper Dih. types, using zeroes
Cleaning up temporary file gromppID2O6e
---
Program grompp, VERSION 3.3.1
Source code file: fatal.c, line: 416

Fatal error:
Too many warnings, /usr/local2/gromacs/bin/grompp terminated
---

"Encountered Subspace Anomaly" (Star Trek)

MD_insu.tpr was not created. Check for errors. Exiting ...

Is there a way to fix it ? Also what are those b_, ga_. gd_
corresponds to ??

Ram.




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--


Justin A. Lemkul
Graduate Research Assistant
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: gmx-users Digest, Vol 50, Issue 97

[eladp]

Try installing development version: openmotif-devel



Hi

I want to use grace 5.1.9 (normally xmvgr). each time i do installation
using " ./configure", it prompts motif not found .

So i tried to find free softare openmotif (it can do the same work as
motif). Having successfully installed openmotif , the grace installation ,
however, still tells me motif not found .
Gromacs 's web page proposes lesstif can also do as motif , so i downloaded
lesstif and installed it succefully , but grace prompted modtif not found
once again.
BTW: my OS is Fedora core 8

Can anyone give a good idear of installing grace..




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Re: [gmx-users] step size too small

[Tsjerk Wassenaar]

Minnale,

Please do read the following:

http://wiki.gromacs.org/index.php/Errors

This one's in there.

Tsjerk


On Mon, Jun 30, 2008 at 11:26 AM, minnale <[EMAIL PROTECTED]> wrote:
>
> Hi all,
> 1) I have embedded protein into popcbilayer
> 2) Energy minimisation
> 3) Later added ions by using genion,
> 4) When I am trying to run minimisation its showing following sentences
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 100
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 49 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -2.1825061e+05
> Maximum force=  4.3672461e+03 on atom 7008
> Norm of force=  5.5597691e+04
>
>
> my .mdp file is
> cpp= /usr/bin/cpp
> define  =  -DFLEX_SPC
> constraints=  none
> integrator  =  steep
> nsteps  =  500
> ;
> ;  Energy minimizing stuff
> ;
> emtol  =  100
> emstep  =  0.01
> nstcomm=  1.0
> ns_type=  grid
> rlist  =  1.0
> rcoulomb=  1.0
> rvdw=  1.0
>
> When I run minimisation before adding ions it ran fine but later not why?
> I have searched about solve this problem in archives list and I understood
> that this not an error. Can I proceed further simulations
> Any comments will be appreciated.
>
> Thanks in advance.
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] step size too small

[minnale]

  
Hi all, 
 1) I have embedded protein into popcbilayer
2) Energy minimisation 
3) Later added ions by using genion, 
4) When I am trying to run minimisation its showing following sentences

 Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 49 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -2.1825061e+05
Maximum force =  4.3672461e+03 on atom 7008
Norm of force =  5.5597691e+04


my .mdp file is
cpp = /usr/bin/cpp
define  =  -DFLEX_SPC
constraints =  none
integrator  =  steep
nsteps  =  500
;
;   Energy minimizing stuff
;
emtol   =  100
emstep  =  0.01
nstcomm =  1.0
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0

When I run minimisation before adding ions it ran fine but later not why?
I have searched about solve this problem in archives list and I understood that 
this not an error. Can I proceed further simulations
Any comments will be appreciated. 

Thanks in advance.


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[gmx-users] RE: anyone knows how to install grace?

[Vitaly Chaban]

> Gromacs 's web page proposes lesstif can also do as motif , so i downloaded
> lesstif and installed it succefully , but grace prompted modtif not found
> once again.
> BTW: my OS is Fedora core 8
> 
> Can anyone give a good idear of installing grace..

I'm using grace on Ubuntu 8.04 and it runs excellently.

I think you have to find a right package for your system.

-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svobody sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban

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Re: [gmx-users] tpbconv functionality

[Tsjerk Wassenaar]

Hi Cesar,

Not with tpbconv. You can do it with grompp, adding the .trr end .edr
file you have as input and making sure that you don't generate new
velocities and set unconstrained_start to yes.

Cheers,

Tsjerk

On Sun, Jun 29, 2008 at 10:18 PM, Cesar Avila <[EMAIL PROTECTED]> wrote:
> I found the tpbconv tool very usefull for generating tpr files for
> resuming the simulations. Nevertheless I couldn't find an option to
> set/change the number of processors to use as the -np option in grompp. Is
> there a way to do this?
>
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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