[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology
ahmet yıldırım
ahmedo047 at gmail.com
Sat Apr 16 10:05:57 CEST 2011
Dear Justin,
I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for eachEDO
molecule using prodrg web server. Then I created 6 .itp files as EDO1.itp,
EDO2.itp.....EDO6.itp. I changed residue numbers. But I have Fatal Error
"moleculetype EDO is redefined". Am I on the wrong track?:-(
*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> 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>> 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>>>
>>
>>
>>
>>
>> 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> | (540)
>>
>> 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto: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
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
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>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
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>
--
Ahmet YILDIRIM
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