ahmet yıldırım wrote:
Dear Justin,
Now, I added two PO4 to the coordinate file, then added two to the
topology. I created PO4_1.gro and PO4_1.itp for first PO4 using PRODRG.
Then, I created PO4_2.gro and PO4_2.itp for first PO4 using PRODRG. I
added 10 atoms/lines into conf.gro from PO4.gro(5cordinate and PO4_2.gro
files (5 coordinate), then 10 the second line of conf.gro. I used only
one because of the same as PO4_1.itp and PO4_2.itp files.
That's exactly what you want to do - an .itp defines a [moleculetype]. If you
have two identical molecules that are defined by the same [moleculetype], you
don't want to #include the same thing twice. In fact, grompp will throw a fatal
error that your [moleculetype] is redefined. Think of this analogy - you
#include "spc.itp" in your system, but you don't do it for every single water
molecule individually. You define the [moleculetype] and then define in the
topology how many instances of that particular molecule in the [molecules]
directive.
*_First PO4 from 3HTB:_*
HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70
13.01 P
HETATM 1367 O1 PO4 A 165 16.899 -26.359 11.761 0.70
8.42 O
HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281 0.70
12.47 O
HETATM 1369 O3 PO4 A 165 15.071 -28.010 11.811 0.70
11.58 O
HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543 0.70
11.36 O
*_second PO4 from 3HTB:_*
HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50
20.49 P
HETATM 1372 O1 PO4 A 166 23.073 -0.065 -18.917 0.50
18.04 O
HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50
19.25 O
HETATM 1374 O3 PO4 A 166 20.616 -0.014 -19.484 0.50
14.22 O
HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50
15.77 O
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
*WARNING 1* [file topol.top, line 10673]:
670 non-matching atom names
atom names from topol.top will be used
atom names from solvated.gro will be ignored
As I said in my last message, the order of the contents of the coordinate file
and [molecules] directive must match. You have not satisfied this requirement.
*WARNING 2* [file em.mdp]:
The sum of the two largest charge group radii (7.005889) is larger than
rlist (1.000000
I have no idea what might cause this other than you've mangled the coordinates
in some way, or perhaps molecules are broken across periodic boundaries. In a
normal input file, the latter is not the case. My guess is that your
copying/pasting of coordinates is somehow at fault.
-Justin
*NOTE 1* [file topol.top, line 10673]:
System has non-zero total charge: 2.000001e+00
*Fatal error:*
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
18 Nisan 2011 23:26 tarihinde Justin A. Lemkul <[email protected]
<mailto:[email protected]>> yazdı:
You said you added one PO4 to the coordinate file, but then added
two to the topology. Hence the difference of exactly 5 atoms, or
one PO4 molecule.
The content of the coordinate file must always match the content of
the topology, with respect to the number of atoms (based on the
listing of molecules) and the order in which they appear in the
[molecules] directive.
-Justin
2011/4/18 lucioric <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>
You need to get or calculate parameters for phosphate. These
parameters are yet calculated for the AMBER forcefield, there
are in
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/frcmod.phos.
You need to install AmberTools and copy the frcmod.phos file
in the
URL above to the appropriate directory (see the AmberTools
manual).
Then, you can build the topology and coordinate files in AMBER
format for your system using the tleap tool. These files in AMBER
format can be converted to Gromacs format using the acpype
program.
With these files in Gromacs format you can run a MD in Gromacs,
using the Amber forcefield.
Lucio Montero
Instituto de Biotecnologia, UNAM, Mexico.
On Mon, 18 Apr 2011 20:40:49 +0300, ahmet yıldırım
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
Dear Justin,
You prepared a useful tutorial. if you used PO4 ligand
(which has 2
molecule) instead of 1JZ4 ligand from 3HTB.pdb, Then, in the
.itp and
.gro files of ligand because of 2 molecule, what change?
Can you give some hint?
Thanks
3HTB.pdb
....
TER 1365 ASN A 163
HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70 13.01 P
HETATM 1367 O1 PO4 A 165 16.899 -26.359 11.761 0.70 8.42 O
HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281 0.70 12.47 O
HETATM 1369 O3 PO4 A 165 15.071 -28.010 11.811 0.70 11.58 O
HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543 0.70 11.36 O
HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50 20.49 P
HETATM 1372 O1 PO4 A 166 23.073 -0.065 -18.917 0.50 18.04 O
HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50 19.25 O
HETATM 1374 O3 PO4 A 166 20.616 -0.014 -19.484 0.50 14.22 O
HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50 15.77 O
HETATM 1376 C4 JZ4 A 167 24.294 -24.124 -0.071 1.00 16.39 C
..
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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
========================================
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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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