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