francesca vitalini wrote:
Thanks Tsjerk, Florian,
However I need the .gro file for the reverse transformation and I
cannot simply obtain it through pdb2gmx as it won't recognize the
atoms
Use editconf to convert between .pdb and .gro (as well as other formats).
pdb2gmx is for producing topologies, not interconverting coordinate files.
-Justin
Fatal error:
Atom BB in residue ALA 1 was not found in rtp entry ALA with 8 atoms
while sorting atoms.
.
Any help with that?
Thanks a lot
2012/2/20 Dommert Florian <domm...@icp.uni-stuttgart.de>:
On Mon, 2012-02-20 at 16:05 +0100, francesca vitalini wrote:
Just one last question Tsjerk, I was trying to load the cg.gro file
obtained with martinize in vmd and the program says it is unable to
load the molecule. the result of the martinize script looks like:
MODEL 1
TITLE Protein in water
CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1
ATOM 1 BB ALA 1 15.063 17.501 13.232 1.00 0.00
ATOM 2 BB GLU 2 14.568 13.732 14.199 1.00 0.00
ATOM 3 SC1 GLU 2 17.373 14.208 15.223 1.00 0.00
TER
ENDMDL
This looks like a PDB file. If you load cg.gro into VMD it will
recognize it as GRO file, but you provide the wrong format. Rename
cg.gro to cg.pdb and it should be loaded successfully into VMD.
/Flo
Does it sound right to you?
Thanks
2012/2/20 francesca vitalini <francesca.vitalin...@gmail.com>:
Thank you so much.. Now it is working. I was trying to do it without
specifying the secondary structure as I'm having problems with the
do_dssp command. It is not working basically and I have to use pdb2gmx
to convert into pdb then go to the dssp webpage and create the dssp
file from there through the pdb. Do you know a fastest way to make it
work? Thanks
However, my Martini account never worked, don't know why, so I cannot
post it directly.
2012/2/20 Tsjerk Wassenaar <tsje...@gmail.com>:
Hey Francesca,
Now there's a small bug in the program. Sorry about it. We'll put the
fixed version on in a bit. The problem arises because you don't
specify the secondary structure and pymol is not yet available for
doing so. The workaround is to explicitly set the secondary structure
to loop, by adding "-ss LLL" on the command line. Thanks for pointing
that out.
By the way, you might want to post these issues on the Martini forum:
http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum
It's not exactly Gromacs...
Cheers,
Tsjerk
On Mon, Feb 20, 2012 at 2:34 PM, francesca vitalini
<francesca.vitalin...@gmail.com> wrote:
Done while waiting for your e-mail. the error message now says
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in
the MDP file
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 1 chains:
INFO 1: (Protein), 25 atoms in 3 residues.
INFO Total size of the system: 3 residues.
Traceback (most recent call last):
File "./martinize-1.0.py", line 2415, in <module>
elif options["-pymol"]:
KeyError: '-pymol'
and the pdb looks like
TITLE Protein in water
REMARK THIS IS A SIMULATION BOX
CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00
ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00
ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00
ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00
ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00
ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00
ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00
ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00
ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00
ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00
ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00
ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00
ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00
ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00
ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00
ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00
ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00
ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00
ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00
ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00
ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00
ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00
ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00
ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00
ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00
TER
can you please explain which the problem is to me?
thanks
2012/2/20 Tsjerk Wassenaar <tsje...@gmail.com>:
Hi Francesca,
Given the error, it seems there's still a mismatch between the number
of atoms and the number indicated. Try converting your structure to
PDB and use that for coarsegraining.
Cheers,
Tsjerk
On Mon, Feb 20, 2012 at 2:08 PM, francesca vitalini
<francesca.vitalin...@gmail.com> wrote:
I've changed that but it is still complaining...
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in
the MDP file
INFO Read input structure from file.
INFO Input structure is a GRO file. Chains will be labeled consecutively.
Traceback (most recent call last):
File "./martinize-1.0.py", line 2306, in <module>
for title,atoms,box in frameIterator(inStream):
File "./martinize-1.0.py", line 1183, in groFrameIterator
atoms = [groAtom(streamIterator.next()) for i in range(natoms)]
File "./martinize-1.0.py", line 1170, in groAtom
return (S(a[10:15]), S(a[5:10]), I(a[:5]), " ",
10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44]))
ValueError: invalid literal for int() with base 10: '2.'
2012/2/20 Tsjerk Wassenaar <tsje...@gmail.com>:
Hi Francesca,
The problem is that the second line of your gro file indicates there
are 2410 atoms in the file, while there are only 25. Did you manually
remove water? In that case you have to update the number of atoms in
the second line. The error message should be more explanatory though.
Cheers,
Tsjerk
On Mon, Feb 20, 2012 at 1:57 PM, francesca vitalini
<francesca.vitalin...@gmail.com> wrote:
I was using the one available from the tutorial but now I have
downloaded the new one and it gives me still an error message like
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in
the MDP file
INFO Read input structure from file.
INFO Input structure is a GRO file. Chains will be labeled consecutively.
Traceback (most recent call last):
File "./martinize-1.0.py", line 2306, in <module>
for title,atoms,box in frameIterator(inStream):
File "./martinize-1.0.py", line 1183, in groFrameIterator
atoms = [groAtom(streamIterator.next()) for i in range(natoms)]
File "./martinize-1.0.py", line 1170, in groAtom
return (S(a[10:15]), S(a[5:10]), I(a[:5]), " ",
10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44]))
ValueError: invalid literal for int() with base 10: '2.'
I have used the command line ./martinize-1.0.py -f npt_strip_wat.gro
-o frag_npt_cg_pdb.top -x frag_npt_cg_pdb.gro -v -p backbone
were my input file is very simply
Protein in water
2410
1ALA N 1 1.497 1.862 1.290 0.1206 -0.3069 -0.2102
1ALA H1 2 1.409 1.866 1.338 0.8590 -0.1748 1.1978
1ALA H2 3 1.547 1.948 1.296 2.0372 -1.4201 0.8359
1ALA H3 4 1.483 1.837 1.194 1.8924 -0.0993 -0.5621
1ALA CA 5 1.585 1.753 1.335 -0.1231 -0.2165 0.4955
1ALA CB 6 1.625 1.781 1.480 0.3554 -0.5405 0.4275
1ALA C 7 1.517 1.617 1.323 0.1234 -0.2807 -0.1917
1ALA O 8 1.407 1.624 1.268 -0.0033 0.4302 0.1378
2GLU N 9 1.566 1.515 1.393 -0.2655 -0.2542 0.1191
2GLU H 10 1.655 1.536 1.434 0.1561 0.1079 -0.9482
2GLU CA 11 1.501 1.384 1.402 0.3096 -0.5394 0.1823
2GLU CB 12 1.601 1.272 1.427 0.7527 -0.2033 -0.0775
2GLU CG 13 1.694 1.280 1.548 -0.0279 0.1789 0.5017
2GLU CD 14 1.779 1.405 1.571 0.4664 -0.1532 0.4921
2GLU OE1 15 1.882 1.412 1.500 0.2904 -0.0189 0.2469
2GLU OE2 16 1.740 1.489 1.654 0.2746 0.1001 0.1509
2GLU C 17 1.378 1.355 1.489 0.5085 -0.1385 0.5964
2GLU O 18 1.352 1.237 1.510 0.3837 -0.1792 0.2200
3GLU N 19 1.307 1.458 1.535 -0.1887 -0.4392 0.2009
3GLU H 20 1.315 1.547 1.489 -1.1961 0.1298 1.0835
3GLU CA 21 1.180 1.436 1.604 -0.3118 -0.2722 0.0307
3GLU CB 22 1.192 1.426 1.757 -0.3397 0.1329 0.0602
3GLU C 23 1.066 1.533 1.572 -0.3117 -0.4554 -0.5274
3GLU O1 24 1.072 1.606 1.471 0.0488 0.2651 0.0047
3GLU O2 25 0.965 1.542 1.646 -0.1745 -0.2606 -0.3621
2.91477 2.91477 2.91477
Can you help me on that?
Thanks
2012/2/20 Tsjerk Wassenaar <tsje...@gmail.com>:
Hi Francesca,
Is this the latest version
(http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)?
If it is, please send me the input file and I'll fix the bug. Note
that the previous version that was available online was one used in a
workshop, while the script was still in beta.
Cheers,
Tsjerk
On Mon, Feb 20, 2012 at 10:43 AM, francesca vitalini
<francesca.vitalin...@gmail.com> wrote:
Hi all,
I'm trying to coarsegrain my structure using the script martinize.py
and using my gro file as inmput and the dssp file with the second
structure downloaded from http://swift.cmbi.ru.nl/gv/dssp using the
pdb structure as input, I get the following error message that I
really don't understand.
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in
the MDP file
INFO Read input structure from file.
INFO Input structure is a GRO file. Chains will be labeled consecutively.
Traceback (most recent call last):
File "./martinize.py", line 2037, in <module>
for title,atoms,box in frameIterator(inStream):
File "./martinize.py", line 1303, in groFrameIterator
atoms = [groAtom(streamIterator.next()) for i in range(natoms)]
File "./martinize.py", line 1290, in groAtom
return (S(a[10:15]), S(a[5:10]), I(a[:5]), " ",
10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44]))
ValueError: invalid literal for int() with base 10: '2.'
Can anyone help me on that?
Thanks
--
Francesca
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Arnimallee 6 14195 Berlin
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========================================
Justin A. Lemkul
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Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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