Hi Justin,
That is really confusing. I tried to run this PDB file many times. But
still I could not get it the topology file. I waited for so long (10
hrs)but still the code looks in a deadlock.
Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat
Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum charges
9: Encad all-atom force field, using full solvent charges
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading JUsti.pdb...
Read 'Tolene.pdb', 7 atoms
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 7 atoms
chain #res #atoms
1 ' ' 1 7
All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp
Atomtype 1
[1]+ Stopped
REMARK This PDB file is created by CS Chem3D
REMARK
COMPND Tolene.pdb
ATOM 1 CB PHE 1 -1.158 0.001 0.000 C
ATOM 2 CG PHE 1 -1.158 -1.336 0.000 C
ATOM 3 CD1 PHE 1 -0.000 -2.004 0.000 C
ATOM 4 CD2 PHE 1 1.158 -1.336 0.000 C
ATOM 5 CE1 PHE 1 1.158 0.001 0.000 C
ATOM 6 CE2 PHE 1 -0.000 0.670 0.000 C
ATOM 7 CZ PHE 1 -0.000 2.167 0.000 C
END
can you please tell me what modifications you have done so that your
pdb2gmx works fine.
thank you for your time
Rob
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
tekle...@ualberta.ca wrote:
Hi Justin,
Thank you pointing out that!
I made all the changes and still cannot go past this line.
REMARK This PDB file is created by CS Chem3D
REMARK
COMPND Tolene.pdb
HETATM 1 CB PHE 0 -1.158 0.001 0.000
C
HETATM 2 CG PHE 0 -1.158 -1.336 0.000
C
HETATM 3 CD1 PHE 0 -0.000 -2.004 0.000
C
HETATM 4 CD2 PHE 0 1.158 -1.336 0.000
C
HETATM 5 CE1 PHE 0 1.158 0.001 0.000
C
HETATM 6 CE2 PHE 0 -0.000 0.670 0.000
C
HETATM 7 CZ PHE 0 -0.000 2.167 0.000
C
END
As you can see I used this PDB file but still no topology out put.
Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum charges
9: Encad all-atom force field, using full solvent charges
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading tolene.pdb...
Read 'Tolene.pdb', 7 atoms
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 7 atoms
chain #res #atoms
1 ' ' 1 7
All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp
Atomtype 1
Is this actually where pdb2gmx stops? There's no fatal error here,
the program should continue to run, at least until it prints out a
real error message. Your .pdb file works fine, I just ran it
through pdb2gmx myself.
-Justin
best
Rob
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
tekle...@ualberta.ca wrote:
Hi Justin,
It does not work. I eliminated the hydrogen atoms and check the
entire .pdb file but could not solve the problem.
the modified PDB file.
REMARK This PDB file is created by CS Chem3D
REMARK
COMPND Tolene.pdb
HETATM 1 CB PHE 0 -1.158 0.001 0.000
CH2
HETATM 2 CG PHE 0 -1.158 -1.336 0.000
C
HETATM 3 CD1 PHE 0 -0.000 -2.004 0.000
CR1
HETATM 4 CD2 PHE 0 1.158 -1.336 0.000
CR1
HETATM 5 CE1 PHE 0 1.158 0.001 0.000
CR1
HETATM 6 CE2 PHE 0 -0.000 0.670 0.000
CR1
HETATM 7 CZ PHE 0 -0.000 2.167 0.000
CR1
END
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading Tolene.pbd.gro...
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
Tolene.pbd.gro
-------------------------------------------------------
"It's So Lonely When You Don't Even
Any comment on that.
It's a pretty obvious typo; .pbd != .pdb.
-Justin
Rob
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
tekle...@ualberta.ca wrote:
Dear Justin,
It really help all the feedback you gave me and thank you for that,.
I have one issues as well.
I try to generate the topology file the way you recommend me
using the pdb2gro but failed to get both the topology and
gromacs file.
This is my Toluene file in pdb file
REMARK This PDB file is created by CS Chem3D
REMARK
COMPND Tolene.pdb
HETATM 1 CB PHE 0 -1.158 0.001 0.000
C
HETATM 2 CG PHE 0 -1.158 -1.336 0.000
C
HETATM 3 CD1 PHE 0 -0.000 -2.004 0.000
C
HETATM 4 CD2 PHE 0 1.158 -1.336 0.000
C
HETATM 5 CE1 PHE 0 1.158 0.001 0.000
C
HETATM 6 CE2 PHE 0 -0.000 0.670 0.000
C
HETATM 7 CZ PHE 0 -0.000 2.167 0.000
C
HETATM 8 H16 PHE 0 -2.111 0.551 0.000
H
HETATM 9 H17 PHE 0 -2.111 -1.886 0.000
H
HETATM 10 H18 PHE 0 -0.000 -3.104 0.000
H
HETATM 11 H19 PHE 0 2.110 -1.886 0.000
H
HETATM 12 H20 PHE 0 2.110 0.551 0.000
H
HETATM 13 H21 PHE 0 1.049 2.538 0.000
H
HETATM 14 H22 PHE 0 -0.524 2.537 -0.909
H
HETATM 15 H23 PHE 0 -0.525 2.537 0.909
H
END
I run
pdb2gmx -ff G43a1 -f TOL.pdb -o TOL.gro -p TOL.top -missing
but I go the following error.
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading YY.pdb...
Read 'Tolene.pdb', 15 atoms
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 15 atoms
chain #res #atoms
1 ' ' 1 15
All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp
Atomtype 1
I tried many times but could not get the topology file.
Can you comment on this please.
What you've shown isn't an error. It reflects the fact that you
don't even have occupancy values in this .pdb file. You will
certainly have a nomenclature problem, though - your H atoms are
not named according to what the .rtp file expects, so you'll
either need to delete the H atoms and let pdb2gmx rebuild them
from the .hdb entries, or use -ignh.
-Justin
Rob
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
tekle...@ualberta.ca wrote:
Dear Gromacs Users,
I have encountered the following issues while I was running
my MD simulation. Can anybody comment on what the meaning of
these notes are. Is there anything I could do to avoid them.
NOTE 2 [file PAP.top, line unknown]:
The largest charge group contains 12 atoms.
Since atoms only see each other when the centers of geometry
of the charge
groups they belong to are within the cut-off distance, too
large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a
few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH,
CO2, CO, etc.
My SOLVENT IS TOLUENE --- the PRODRG gave me a topology file
with only one group charge only.
That's almost certainly wrong. See, for instance, the PHE
side chain in the relevant .rtp entry for a more reasonable
charge group setup. If you're using PRODRG defaults, then the
charges are probably unsatisfactory, as well.
The rationale for the charge group size is summed up here:
http://lists.gromacs.org/pipermail/gmx-users/2008-November/038153.html
NOTE 1 [file nvt.mdp, line unknown]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale
thermostat.
See the literature about this one, as well as the numerous
list archive discussions. For initial equilibration, a weak
coupling scheme is probably fine, but you can also use
V-rescale. Also of interest:
http://www.gromacs.org/Documentation/Terminology/Thermostats
NOTE 3 [file aminoacids.dat, line 1]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing
This all depends on the size of your system, how much of the
work is distributed between the real-space Coulombic
interaction and PME.
In addition to the above notes I have also some questions
about the NVT and NPT simulation.
1)I am using toluene as a solvent to simulate my polymer, do
I need to use the compressibility of toluene which is 9.2e-5
or the default value 4.5e-5 1/bar.
Well, 4.5e-5 corresponds to water, which you aren't using...
For NVT, this won't matter since the box is fixed, but for
NPT, the compressibility will affect the response of your
system to pressure. The differences may be minimal, but if
you know the right value, why accept a wrong one?
2)What about the dielectric constant (the dielectric constant
for toluene is 2-2.4), but the default value is 80 ( I assume
this is for water- am I right).
Yes, the default again assumes water as the solvent.
3)Is always rvdw = 1.4 nm for GROMOS96. As a result I have
to increase my box size of the solute at the beginning to a
min of 2*1.4 =2.8 ( min image convection). Is this the right
way to do!
At an absolute minimum. Keep in mind that the box vectors
will fluctuate under NPT, so if the box decreases even a
little bit below 2.8, you will be violating the minimum image
convention.
4)I run an NVT simulation to equilibrate my system for 100
ps. When I checked my simulation at the end (successfully
completed) I noticed that the shape of my simulation box
looks CIRCULAR! some how the rectangular shape looks
distorted. What does this tell! Do you guys think something
is wrong in my simulation.
This could be some visualization artifact, or the components
of your system have condensed within the box. Without
actually seeing it, it's hard to tell. If you post an image
online (Photobucket, etc) then we might get a better sense of
what's going on.
5)I included the polar and aromatic hydrogens in my
simulation ( ffG43a1.itp - GROMOS96.1 in PRODRG). Does these
hydrogen influence my result as the force field is a united
atom force field. Or How can I get rid of them if I want.
With or without the aromatic hydrogen gave good results (
besides lower computational cost). Does Gromos96 model
correctly aromatic-Aromatic interaction.
Well, "correct" is a relative term for all force fields, but
you need to follow the prescribed setup of the force field
itself, otherwise you can throw it all away. If you lump the
hydrogens into the ring carbons and have an uncharged ring,
the result will be different than if you have the hydrogens
there with a small charge on each C and H. Again, refer to
the force field .rtp file for examples. You can also create a
better toluene topology by renaming the residue in your
coordinate file PHE and trick pdb2gmx:
pdb2gmx -f toluene.pdb -missing
Then change the mass of the CH2 group (which pdb2gmx thinks is
a CB for PHE) to reflect a CH3 group. Make an .itp file out
of the resulting .top by removing the unnecessary #includes,
[system], and [molecule] directives. Then you don't have to
worry about messing with PRODRG. I should note, as well, that
this is about the only appropriate use of -missing I can think
of at the moment (just for clarity in the archives; I usually
warn against using -missing).
-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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--
========================================
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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--
========================================
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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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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