[gmx-users] protein-ligand complex tutorial
ahmet yıldırım
ahmedo047 at gmail.com
Mon Apr 18 23:58:14 CEST 2011
Dear Justin,
I rearranged conf.gro but Gromacs is giving the same errors again. I think I
am going mad :-(
*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 <jalemkul at vt.edu> 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 <jalemkul at vt.edu <mailto:
>> jalemkul at vt.edu>> 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 <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>>
>> <mailto:jalemkul at vt.edu>>> 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 <lucioric at ibt.unam.mx
>> <mailto:lucioric at ibt.unam.mx>
>> <mailto:lucioric at ibt.unam.mx
>> <mailto:lucioric at ibt.unam.mx>> <mailto:lucioric at ibt.unam.mx
>>
>> <mailto:lucioric at ibt.unam.mx>
>>
>> <mailto:lucioric at ibt.unam.mx <mailto:lucioric at ibt.unam.mx
>> >>>>
>>
>>
>>
>> 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
>> <ahmedo047 at gmail.com <mailto:ahmedo047 at gmail.com>
>> <mailto:ahmedo047 at gmail.com <mailto:ahmedo047 at gmail.com>>
>> <mailto:ahmedo047 at gmail.com <mailto:ahmedo047 at gmail.com>
>> <mailto:ahmedo047 at gmail.com <mailto:ahmedo047 at gmail.com>>>> 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
>>
>> ..
>>
>>
>> -- gmx-users mailing list gmx-users at gromacs.org
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>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org
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>> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>>>
>>
>>
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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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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>
--
Ahmet YILDIRIM
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