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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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