[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Apr 16 11:15:22 CEST 2011
On 16/04/2011 6:05 PM, ahmet yıldırım wrote:
> Dear Justin,
>
> I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for
> each EDO moleculeusing prodrg web server. Then I created 6 .itp files
> as EDO1.itp, EDO2.itp.....EDO6.itp.
Why? The fragment
[molecules]
EDO 6
is what specifies six identical EDO molecules.
Your earlier problem was in matching the contents of your [molecules]
section with your coordinate file. They have to contain the same
molecules in the same order.
> I changed residue numbers. But I have Fatal Error "moleculetype EDO is
> redefined". Am I on the wrong track?:-(
So don't re-define moleculetype EDO.
Mark
>
> _*EDO1.itp:*_
> [ moleculetype ]
> ; Name nrexcl
> EDO 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OA 1 EDO O1 1 -0.163 15.9994
> 2 H 1 EDO HAA 1 0.074 1.0080
> 3 CH2 1 EDO C1 1 0.089 14.0270
> 4 CH2 1 EDO C2 2 0.089 14.0270
> 5 OA 1 EDO O2 2 -0.163 15.9994
> 6 H 1 EDO HAB 2 0.074 1.0080
>
> *_EDO2.itp:_*
> [ moleculetype ]
> ; Name nrexcl
> EDO 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OA 2 EDO O1 1 -0.163 15.9994
> 2 H 2 EDO HAA 1 0.074 1.0080
> 3 CH2 2 EDO C1 1 0.089 14.0270
> 4 CH2 2 EDO C2 2 0.089 14.0270
> 5 OA 2 EDO O2 2 -0.163 15.9994
> 6 H 2 EDO HAB 2 0.074 1.0080
> _*topol.top*_:
> ...
> #include "EDO1.itp"
> #include "EDO2.itp"
> #include "EDO3.itp"
> #include "EDO4.itp"
> #include "EDO5.itp"
> #include "EDO6.itp"
> #include "TRS.itp"
> ...
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Protein_chain_B 1
> EDO 6
> TRS 1
> SOL 185
> SOL 143
> SOL 33713
>
> _*conf.gro:*_
> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
> 5384
> 2GLN N 1 1.458 -1.158 0.739
> 2GLN H1 2 1.520 -1.083 0.763
> ....
>
> 485HOH HW1 5333 0.221 -3.864 -2.291
> 485HOH HW2 5334 0.303 -3.946 -2.407
> 1EDO O1 1 0.625 -3.071 -0.171
> 1EDO HAA 2 0.698 -3.048 -0.107
> 1EDO C1 3 0.596 -3.211 -0.163
> 1EDO C2 4 0.486 -3.247 -0.261
> 1EDO O2 5 0.365 -3.179 -0.224
> 1EDO HAB 6 0.292 -3.203 -0.288
> 2EDO O1 1 2.023 -4.300 0.220
> 2EDO HAA 2 2.046 -4.296 0.317
> 2EDO C1 3 2.138 -4.342 0.146
> 2EDO C2 4 2.096 -4.347 -0.001
> 2EDO O2 5 2.196 -4.412 -0.079
> 2EDO HAB 6 2.167 -4.415 -0.174
> 3EDO O1 1 2.502 -3.407 -2.265
> 3EDO HAA 2 2.529 -3.365 -2.178
> 3EDO C1 3 2.466 -3.303 -2.359
> 3EDO C2 4 2.424 -3.364 -2.492
> 3EDO O2 5 2.294 -3.423 -2.477
> 3EDO HAB 6 2.265 -3.464 -2.564
> 4EDO O1 1 1.021 -5.733 -2.007
> 4EDO HAA 2 0.952 -5.780 -2.061
> 4EDO C1 3 0.995 -5.753 -1.868
> 4EDO C2 4 1.102 -5.679 -1.787
> 4EDO O2 5 1.091 -5.540 -1.816
> 4EDO HAB 6 1.160 -5.489 -1.764
> 5EDO O1 1 1.988 -3.117 -3.247
> 5EDO HAA 2 1.915 -3.177 -3.217
> 5EDO C1 3 2.100 -3.194 -3.291
> 5EDO C2 4 2.212 -3.102 -3.337
> 5EDO O2 5 2.247 -3.012 -3.231
> 5EDO HAB 6 2.321 -2.952 -3.261
> 6EDO O1 1 0.987 -4.579 -0.020
> 6EDO HAA 2 0.969 -4.622 -0.109
> 6EDO C1 3 1.118 -4.521 -0.021
> 6EDO C2 4 1.145 -4.456 0.114
> 6EDO O2 5 1.054 -4.506 0.212
> 6EDO HAB 6 1.073 -4.463 0.300
> 1TRS O1 1 1.825 -3.900 0.047
> 1TRS HAA 2 1.853 -3.860 -0.040
> 1TRS C1 3 1.712 -3.977 0.028
> 1TRS C 4 1.659 -4.044 0.150
> 1TRS C3 5 1.576 -3.946 0.226
> 1TRS O3 6 1.634 -3.824 0.256
> 1TRS HAC 7 1.569 -3.768 0.307
> 1TRS N 8 1.582 -4.159 0.113
> 1TRS HAE 9 1.547 -4.204 0.195
> 1TRS HAF 10 1.505 -4.131 0.056
> 1TRS HAD 11 1.639 -4.223 0.062
> 1TRS C2 12 1.776 -4.085 0.233
> 1TRS O2 13 1.887 -4.122 0.160
> 1TRS HAB 14 1.961 -4.148 0.222
> 8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550
> 0.00000 0.00000 0.00000
>
> 14 Nisan 2011 21:09 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> yazdı:
>
>
>
> ahmet yıldırım wrote:
>
> Dear Justin,
>
> Thanks for your valuable helps. How should I rearranged the
> conf.gro file for 6 EDO ligand? is the following conf.gro
> mistake?
>
>
> Well, it's certainly not working, is it? You only have one EDO
> molecule shown here. Is this the only one? If it is, then you
> need to build the system to reflect what you actually want to do.
> No one on this list can tell you that. You have to build a
> starting configuration that fits the goals of your study.
>
> -Justin
>
> _*conf.gro:*_
>
> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
> 5354
> 2GLN N 1 1.458 -1.158 0.739
> 2GLN H1 2 1.520 -1.083 0.763
> ...
> 485HOH HW1 5333 0.221 -3.864 -2.291
> 485HOH HW2 5334 0.303 -3.946 -2.407
> 1EDO OAB 1 0.625 -3.071 -0.171
> 1EDO HAA 2 0.698 -3.048 -0.107
> 1EDO CAA 3 0.596 -3.211 -0.163
> 1EDO CAC 4 0.486 -3.247 -0.261
> 1EDO OAD 5 0.365 -3.179 -0.224
> 1EDO HAB 6 0.292 -3.203 -0.288
> 1TRS O1 1 1.825 -3.900 0.047
> 1TRS HAA 2 1.853 -3.860 -0.040
> 1TRS C1 3 1.712 -3.977 0.028
> 1TRS C 4 1.659 -4.044 0.150
> 1TRS C3 5 1.576 -3.946 0.226
> 1TRS O3 6 1.634 -3.824 0.256
> 1TRS HAC 7 1.569 -3.768 0.307
> 1TRS N 8 1.582 -4.159 0.113
> 1TRS HAE 9 1.547 -4.204 0.195
> 1TRS HAF 10 1.505 -4.131 0.056
> 1TRS HAD 11 1.639 -4.223 0.062
> 1TRS C2 12 1.776 -4.085 0.233
> 1TRS O2 13 1.887 -4.122 0.160
> 1TRS HAB 14 1.961 -4.148 0.222
>
> 8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550
> 0.00000 0.00000 0.00000
>
> 14 Nisan 2011 20:15 tarihinde Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> yazdı:
>
>
>
>
> ahmet yıldırım wrote:
>
> Dear Justin,
>
> I built .rtp entries for two ligands using
> (http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the
> topol.top the following parts:
> #include "TRS.itp"
> #include "EDO.itp"
>
>
> Well, either pdb2gmx built the molecules into your topology or
> you're #including them in this manner, you should not do both.
>
> TRS 1
> EDO 6
>
>
> So this is part of your [molecules] directive? If you've
> got six
> copies of EDO, that's likely where the disconnect comes
> from - you
> only had one in your previous coordinate file snippet.
>
>
> Furthermore I added the number of atoms (20) in the
> second line
> of the
>
>
> If you have 6 EDO, the necessary addition is more than just 20.
>
>
> .gro file. may the problem related to pdb file (3NM4.pdb)?
> Because -OH groups seems as -O. isn't it? maybe I'm
> wrong. What
> would you recommend?
>
>
> Generally H atoms are not present in crystal structures.
> If your
> ligands require certain H atoms, then you must do one of
> two things:
>
> 1. Add all the necessary hydrogen atoms to the protein and
> ligands
> and run pdb2gmx.
>
> 2. Have no H atoms present in the initial coordinate file
> and build
> suitable .hdb entries for your ligands so they will be
> constructed
> from existing atoms.
>
> It seems like you're applying several different methods at
> once.
> There are protein-ligand tutorials that you may find
> useful for
> keeping all of this straight (I recommend my own):
>
> http://www.gromacs.org/Documentation/Tutorials#Protein-Ligand_Systems
>
> -Justin
>
> 2011/4/14 Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>
>
>
>
>
> ahmet yıldırım wrote:
>
> Dear users,
>
> pdb2gmx -f xxx.pdb
> water:spc
> forcefield:43a1
> editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
> genbox -cp box.gro -cs spc216.gro -p topol.top -o
> solvated.gro
> grompp -f em.mdp -p topol.top -c solvated.gro -o
> em.tpr
> *Fatal error:*
> number of coordinates in coordinate file
> (solvated.gro,
> 106523)
> does not match topology (topol.top, 106553)
> I look at gmx-user search. But I dont be able to
> solved the
> problem. Then I look at conf.gro and box.gro. I
> recognised the
> there is not the TRS ligand in the box.gro file.
> What reason?
>
>
> Based on your workflow, it looks as is you never
> added it in. If
> conf.gro came from pdb2gmx, did you build .rtp
> entries for your
> ligands, or just #include .itp files after the fact?
> If the
> latter,
> then you have to modify the coordinate file
> (conf.gro) to include
> these molecules. If you did this but did not
> correctly increment
> the number of atoms in the second line of the .gro
> file, likely
> anything with a higher atom number got truncated.
> If the
> conf.gro
> file you show below is indeed what you used, though,
> I see no
> reason
> why this should have happened except that perhaps
> you left out a
> step you thought you had done previously.
>
> The difference in the coordinate file vs. topology
> is 30 atoms,
> which is more than both of your ligands (20 atoms),
> so your
> problem
> likely lies elsewhere.
>
> -Justin
>
>
> Thanks in advance
>
> _*conf.gro:*_
> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
> 5354
> 2GLN N 1 1.458 -1.158 0.739
> 2GLN H1 2 1.520 -1.083 0.763
> ...
> 485HOH HW1 5333 0.221 -3.864 -2.291
> 485HOH HW2 5334 0.303 -3.946 -2.407
> 1EDO OAB 1 0.625 -3.071 -0.171
> 1EDO HAA 2 0.698 -3.048 -0.107
> 1EDO CAA 3 0.596 -3.211 -0.163
> 1EDO CAC 4 0.486 -3.247 -0.261
> 1EDO OAD 5 0.365 -3.179 -0.224
> 1EDO HAB 6 0.292 -3.203 -0.288
> 1TRS O1 1 1.825 -3.900 0.047
> 1TRS HAA 2 1.853 -3.860 -0.040
> 1TRS C1 3 1.712 -3.977 0.028
> 1TRS C 4 1.659 -4.044 0.150
> 1TRS C3 5 1.576 -3.946 0.226
> 1TRS O3 6 1.634 -3.824 0.256
> 1TRS HAC 7 1.569 -3.768 0.307
> 1TRS N 8 1.582 -4.159 0.113
> 1TRS HAE 9 1.547 -4.204 0.195
> 1TRS HAF 10 1.505 -4.131 0.056
> 1TRS HAD 11 1.639 -4.223 0.062
> 1TRS C2 12 1.776 -4.085 0.233
> 1TRS O2 13 1.887 -4.122 0.160
> 1TRS HAB 14 1.961 -4.148 0.222
> 8.13100 7.04165 13.54850 0.00000 0.00000
> -4.06550 0.00000 0.00000 0.00000
>
>
>
>
>
> -- Ahmet YILDIRIM
>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
> <http://vt.edu> | (540)
>
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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>
> -- Ahmet YILDIRIM
>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
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>
>
> --
> Ahmet YILDIRIM
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at
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>
>
> --
> Ahmet YILDIRIM
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