[gmx-users] vmd does not display the molecule

[leila karami]

Hi

I am trying to open a gromacs .gro file with VMD but
VMD gives the following message upon opening and does not display the
molecule : [ error reading box , unexpected end-of-file reached ]

I checked number of atoms specified on the second line of the gro file
and number of atoms really present in the file. It is ok. I also Checked
that the box is correctly described at the last line of my file.

please guied me
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[Justin A. Lemkul]

Post by leila karami
Hi
I am trying to open a gromacs .gro file with VMD but
VMD gives the following message upon opening and does not display the
molecule : [ error reading box , unexpected end-of-file reached ]
I checked number of atoms specified on the second line of the gro file
and number of atoms really present in the file. It is ok. I also Checked
that the box is correctly described at the last line of my file.

Well, if everything is right then you wouldn't have an error :) In any case,
you haven't provided enough tangible evidence to diagnose the issue. If you can
post the first few and last few lines of the .gro file (i.e. "head conf.gro" and
"tail conf.gro"), maybe someone can spot the problem. Also, search the VMD
mailing list, since this error has been posted there before.

-Justin
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

[leila karami]

dear justin

I checked the VMD mailing list but that does not help me.

first few lines of my gro file :

Protein in water
23136
1GLY N 1 1.655 4.898 3.866 -0.3222 -0.2420 0.1437
1GLY CA 2 1.677 4.774 3.793 0.0134 -0.2201 0.2050
1GLY HA1 3 1.579 4.735 3.767 0.5541 -1.5676 0.1443
1GLY HA2 4 1.732 4.708 3.859 1.2946 2.0442 1.5391
1GLY C 5 1.760 4.809 3.671 0.1350 -0.3085 0.2633
1GLY O 6 1.732 4.904 3.598 0.1431 -0.4147 0.1209
2SER N 7 1.867 4.733 3.644 0.3115 -0.0506 0.2274
2SER H 8 1.898 4.660 3.706 -1.4080 -0.0311 1.1663
2SER CA 9 1.924 4.738 3.511 -0.9271 0.2649 -0.3082
2SER HA 10 1.845 4.759 3.439 -0.6670 -0.9431 -0.9674


last few lines of my gro file :

7208Na Na23127 1.251 2.111 2.829 0.0512 -0.5390 0.2230
7209Na Na23128 0.220 2.894 0.285 -0.0656 0.2288 -0.0477
7210Na Na23129 2.803 0.503 5.080 0.0192 -0.1246 0.0370
7211Na Na23130 3.718 2.036 1.304 -0.4850 -0.3162 0.4396
7212Na Na23131 2.322 3.787 2.485 0.2661 0.1734 0.5773
7213Na Na23132 3.592 5.392 5.571 0.4515 0.6877 -0.3284
7214Na Na23133 4.708 2.478 0.651 -0.1105 0.1018 -0.4275
7215Na Na23134 4.612 4.964 0.340 0.2845 -0.3202 0.0326
7216Na Na23135 5.438 6.245 5.071 -0.0165 0.1414 -0.2011
7217Na Na23136 5.855 1.272 5.027 -0.3189 0.4687 -0.1455
6.21600 6.27700 6.26300
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[Justin A. Lemkul]

Post by leila karami
dear justin
I checked the VMD mailing list but that does not help me.

Well, the structure of the .gro file appears intact. Somewhere along the way,
VMD thinks it's hitting the end of the file. Have you manipulated or edited the
file in any way? Opened it using some weird Windows software that saved some
hidden characters or something? If so, you can run it through dos2unix to
correct that.

As an aside, what kind of model are you using? You have explicit HA atoms on
the CA of GLY (OPLS? AMBER?), but no N-terminal protonation. That would seem to
be a completely fictitious and unreasonable model for a standard N-terminal
glycine. Not related to your problem, but I seem to be on a roll of free advice
this morning :)

-Justin

Post by leila karami
Protein in water
23136
1GLY N 1 1.655 4.898 3.866 -0.3222 -0.2420 0.1437
1GLY CA 2 1.677 4.774 3.793 0.0134 -0.2201 0.2050
1GLY HA1 3 1.579 4.735 3.767 0.5541 -1.5676 0.1443
1GLY HA2 4 1.732 4.708 3.859 1.2946 2.0442 1.5391
1GLY C 5 1.760 4.809 3.671 0.1350 -0.3085 0.2633
1GLY O 6 1.732 4.904 3.598 0.1431 -0.4147 0.1209
2SER N 7 1.867 4.733 3.644 0.3115 -0.0506 0.2274
2SER H 8 1.898 4.660 3.706 -1.4080 -0.0311 1.1663
2SER CA 9 1.924 4.738 3.511 -0.9271 0.2649 -0.3082
2SER HA 10 1.845 4.759 3.439 -0.6670 -0.9431 -0.9674
7208Na Na23127 1.251 2.111 2.829 0.0512 -0.5390 0.2230
7209Na Na23128 0.220 2.894 0.285 -0.0656 0.2288 -0.0477
7210Na Na23129 2.803 0.503 5.080 0.0192 -0.1246 0.0370
7211Na Na23130 3.718 2.036 1.304 -0.4850 -0.3162 0.4396
7212Na Na23131 2.322 3.787 2.485 0.2661 0.1734 0.5773
7213Na Na23132 3.592 5.392 5.571 0.4515 0.6877 -0.3284
7214Na Na23133 4.708 2.478 0.651 -0.1105 0.1018 -0.4275
7215Na Na23134 4.612 4.964 0.340 0.2845 -0.3202 0.0326
7216Na Na23135 5.438 6.245 5.071 -0.0165 0.1414 -0.2011
7217Na Na23136 5.855 1.272 5.027 -0.3189 0.4687 -0.1455
6.21600 6.27700 6.26300

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

[Nicolas Sapay]

Hello,

Did you try to just add a blank line at the end of the file? (after the
box definition). Sometimes, that works for me. Otherwise, it could a
problem of bad end-of-line character. That may happen if you have edited
the file on Windows and try to visualize it on Linux.

Nicolas

Post by leila karami
Hi
I am trying to open a gromacs .gro file with VMD but
VMD gives the following message upon opening and does not display the
molecule : [ error reading box , unexpected end-of-file reached ]
I checked number of atoms specified on the second line of the gro file
and number of atoms really present in the file. It is ok. I also
Checked that the box is correctly described at the last line of my file.
please guied me

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[leila karami]

dear justin

I transfer gro files from linux to windows through SSH secure shell program.
I added 10 Na ions by genion command but in gro file following case is
appeared:

7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991
7209Na Na23128 0.179 2.821 0.336 -0.2683 -0.1820 0.5803
7210Na Na23129 2.288 0.458 4.819 -0.1171 0.7612 -0.4903
7211Na Na23130 3.640 1.815 1.138 -0.1083 -0.1591 0.0485
7212Na Na23131 2.183 3.845 1.964 -0.0409 -0.1492 0.6725
7213Na Na23132 3.356 5.216 5.834 -0.2686 0.1059 -0.1660
7214Na Na23133 4.304 2.510 0.809 -0.2994 0.3939 0.7264
7215Na Na23134 4.609 4.931 0.535 -0.2609 0.1315 -0.1767
7216Na Na23135 5.553 6.022 5.152 0.3516 -0.2021 0.2022
7217Na Na23136 5.865 1.114 5.034 0.0442 0.0272 0.3437
*7218Cl Cl23137 0.000 0.000 0.000 0.0000 0.0000 0.0000
* 6.15463 6.21503 6.20117

I deleted line of 7218Cl Cl23137 0.000 0.000
0.000 0.0000 0.0000 0.0000

in top file following case is appeared:
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
SOL 7117
Na 10
Cl 0

I deleted last line.

I am using amber03 force field in gromacs program to study interaction of
pr-dna.
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[Erik Marklund]

Post by leila karami
dear justin
I transfer gro files from linux to windows through SSH secure shell
program. I added 10 Na ions by genion command but in gro file
7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991
7209Na Na23128 0.179 2.821 0.336 -0.2683 -0.1820 0.5803
7210Na Na23129 2.288 0.458 4.819 -0.1171 0.7612 -0.4903
7211Na Na23130 3.640 1.815 1.138 -0.1083 -0.1591 0.0485
7212Na Na23131 2.183 3.845 1.964 -0.0409 -0.1492 0.6725
7213Na Na23132 3.356 5.216 5.834 -0.2686 0.1059 -0.1660
7214Na Na23133 4.304 2.510 0.809 -0.2994 0.3939 0.7264
7215Na Na23134 4.609 4.931 0.535 -0.2609 0.1315 -0.1767
7216Na Na23135 5.553 6.022 5.152 0.3516 -0.2021 0.2022
7217Na Na23136 5.865 1.114 5.034 0.0442 0.0272 0.3437
*7218Cl Cl23137 0.000 0.000 0.000 0.0000 0.0000 0.0000
* 6.15463 6.21503 6.20117
I deleted line of 7218Cl Cl23137 0.000 0.000
0.000 0.0000 0.0000 0.0000
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
SOL 7117
Na 10
Cl 0
I deleted last line.
I am using amber03 force field in gromacs program to study interaction
of pr-dna.

Not sure if it's related, but your topology doesn't match the gro-file.
0 Cl in top, but 1 in gro.

/Erik

[Erik Marklund]

Post by Erik Marklund

Post by leila karami
dear justin
I transfer gro files from linux to windows through SSH secure shell
program. I added 10 Na ions by genion command but in gro file
7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991
7209Na Na23128 0.179 2.821 0.336 -0.2683 -0.1820 0.5803
7210Na Na23129 2.288 0.458 4.819 -0.1171 0.7612 -0.4903
7211Na Na23130 3.640 1.815 1.138 -0.1083 -0.1591 0.0485
7212Na Na23131 2.183 3.845 1.964 -0.0409 -0.1492 0.6725
7213Na Na23132 3.356 5.216 5.834 -0.2686 0.1059 -0.1660
7214Na Na23133 4.304 2.510 0.809 -0.2994 0.3939 0.7264
7215Na Na23134 4.609 4.931 0.535 -0.2609 0.1315 -0.1767
7216Na Na23135 5.553 6.022 5.152 0.3516 -0.2021 0.2022
7217Na Na23136 5.865 1.114 5.034 0.0442 0.0272 0.3437
*7218Cl Cl23137 0.000 0.000 0.000 0.0000 0.0000 0.0000
* 6.15463 6.21503 6.20117
I deleted line of 7218Cl Cl23137 0.000 0.000
0.000 0.0000 0.0000 0.0000
in top file following case is appeared: [ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
SOL 7117
Na 10
Cl 0
I deleted last line.
I am using amber03 force field in gromacs program to study
interaction of pr-dna.

Not sure if it's related, but your topology doesn't match the
gro-file. 0 Cl in top, but 1 in gro.
/Erik

Ignore my previous email. I missed that you deleted the Cl-related
lines. So, did VMD display your system correctly before removing those
lines?

/Erik

[Justin A. Lemkul]

Post by leila karami
dear justin
I transfer gro files from linux to windows through SSH secure shell
program. I added 10 Na ions by genion command but in gro file following

If an unrequested Cl is being added, then that is worth investigating. What was
your *exact* genion command?

Does the VMD error result in the edited file, or the one that has the additional
Cl atom?

Post by leila karami
7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991
7209Na Na23128 0.179 2.821 0.336 -0.2683 -0.1820 0.5803
7210Na Na23129 2.288 0.458 4.819 -0.1171 0.7612 -0.4903
7211Na Na23130 3.640 1.815 1.138 -0.1083 -0.1591 0.0485
7212Na Na23131 2.183 3.845 1.964 -0.0409 -0.1492 0.6725
7213Na Na23132 3.356 5.216 5.834 -0.2686 0.1059 -0.1660
7214Na Na23133 4.304 2.510 0.809 -0.2994 0.3939 0.7264
7215Na Na23134 4.609 4.931 0.535 -0.2609 0.1315 -0.1767
7216Na Na23135 5.553 6.022 5.152 0.3516 -0.2021 0.2022
7217Na Na23136 5.865 1.114 5.034 0.0442 0.0272 0.3437
*7218Cl Cl23137 0.000 0.000 0.000 0.0000 0.0000 0.0000
* 6.15463 6.21503 6.20117
I deleted line of 7218Cl Cl23137 0.000 0.000
0.000 0.0000 0.0000 0.0000
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
SOL 7117
Na 10
Cl 0
I deleted last line.
I am using amber03 force field in gromacs program to study interaction
of pr-dna.

Then I know that your model is wrong. You have no N-terminal protonation
whatsoever! Think about biology before plowing ahead with computer programs
that are only capable of doing what you tell them. Under AMBER, terminal
residues require a prefix, i.e. NGLY (and CXXX for the C-terminal residues).
This has been stated many times across this list, and is clearly in the ffamber
documentation. Did you perhaps use the -missing flag with pdb2gmx when you got
an error message?

Perhaps this extra, unwanted, Cl atom is being added by genion because you have
some bizarre fractional charge on your molecule?

-Justin
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================