[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 14 19:15:42 CEST 2011
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):
> 2011/4/14 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> ahmet yıldırım wrote:
> Dear users,
> pdb2gmx -f xxx.pdb
> 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.
> Thanks in advance
> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
> 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> | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> Ahmet YILDIRIM
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users