ahmet yıldırım wrote:
Dear Justin,
If I send your e-mail the conf.gro, topol.top and PO4.itp files, can you
look at them? do you have a little time?
There are many problems with the files you sent me.
1. The [molecules] section in no way reflects the contents of the system. You
have:
[ molecules ]
; Compound #mols
Protein_chain_A 1
PO4 2
SOL 220
SOL 15025
There are two things wrong here: (a) you have only 220 molecules of water, so
the second SOL block refers to something that doesn't exist and (b) as I have
said several times now, the molecules are listed out of order. In the .gro
file, your two PO4 molecules are listed last, after the protein and water. In
the topology, they follow the protein, but are listed before the water. The
order of the molecules in the coordinate file and [molecules] listing must match
exactly.
2. The spacing of the lines in conf.gro for PO4 is still wrong. Please make
sure to read this message in monospace font so it is clear. You have:
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
The PO4 lines need to be adjusted so that the residue names are aligned
properly, i.e.:
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
The required .gro file format is discussed in the online manual. You must
adhere to it for proper interpretation:
http://manual.gromacs.org/online/gro.html
After making these changes, grompp stops complaining.
-Justin
19 Nisan 2011 00:59 tarihinde Justin A. Lemkul <[email protected]
<mailto:[email protected]>> yazdı:
ahmet yıldırım wrote:
Dear Justin,
I rearranged conf.gro but Gromacs is giving the same errors
again. I think I am going mad :-(
In the absence of the corresponding topology, there is no way to
help you other than to say you're still doing something wrong.
Your coordinates still appear misaligned. I can confirm that the
spacing errors will lead to incorrect coordinate interpretation and
thus the warning about the charge groups.
-Justin
*_conf.gro_*
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
5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750
0.00000 0.00000 0.00000
19 Nisan 2011 00:37 tarihinde Justin A. Lemkul <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>> yazdı:
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]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[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]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[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]>>>
<mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>> <mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>
<mailto:[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]>>>
<mailto:[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>>
<mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
<mailto:[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> <http://vt.edu>
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-- ========================================
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>
<http://vt.edu> | (540)
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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
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--
========================================
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
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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