ahmet yıldırım wrote:
Dear Justin,
But I doesn't see any error in the conf.gro. Am I wrong?
_conf.gro:_
LYSOZYME
2363
1MET N 1 0.556 -1.596 -0.893
...
388HOH HW2 2353 1.763 -1.939 1.371
1PO4 O2 1 1.456 -2.557 1.128
1PO4 P 2 1.543 -2.651 1.204
1PO4 O3 3 1.507 -2.801 1.181
1PO4 O4 4 1.504 -2.632 1.354
1PO4 O1 5 1.690 -2.636 1.176
1PO4 O2 1 2.196 0.201 -1.915
1PO4 P 2 2.174 0.062 -1.865
1PO4 O3 3 2.062 -0.001 -1.948
1PO4 O4 4 2.142 0.066 -1.713
1PO4 O1 5 2.307 -0.006 -1.892
Well, if my monospace font is any indication, yes, you have column misalignment
in the coordinates that could be causing a problem regarding charge group size.
I also don't know if the identical residue number will cause a problem between
your two PO4 molecules, but it might.
The other issue about mismatched atom names is a combination of the coordinate
file and topology not agreeing with respect to their order.
-Justin
5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000
0.00000 0.00000
19 Nisan 2011 00:12 tarihinde Justin A. Lemkul <[email protected]
<mailto:[email protected]>> yazdı:
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]> <mailto:[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]>> <mailto:[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]>>
<mailto:[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> <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 <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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