Hi,

Unfortunately, most of molecular docking softwares are unable to handle metal ions as ligand.

i think you should try pdb format of metal ions for docking

change your ligand file format sdf to pdb

after it please reply me

Hi,

       Actually when convert sdf to pdb/mol2 or any other format metal.pdb have zero charge  while there is+3 charge in sdf  so how to overcome this problem?  For conversion i am using open babel. Is there any other tool or software which is suitable for metal ion?

How can I convert metal ion pdb/mol2 file to pdbqt using autodock?  

          When i convert its give following errors

Python 2.5.6 (r256:88840, Nov 6 2012, 15:29:26)

[GCC 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)] on linux2

Type "copyright", "credits" or "license()" for more information.

****************************************************************

Personal firewall software may warn about the connection IDLE

makes to its subprocess using this computer's internal loopback

interface. This connection is not visible on any external

interface and no data is sent to or received from the Internet.

****************************************************************

IDLE 1.2.6 ==== No Subprocess ====

>>> cd+2:A:LIG:CD and cd+2:A:LIG:CD have the same coordinates

ERROR *********************************************

Traceback (most recent call last):

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/ViewerFramework/VF.py", line 898, in tryto

result = command( *args, **kw )

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/autotorsCommands.py", line 867, in doit

initLPO4(mol, cleanup=cleanup)

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/autotorsCommands.py", line 292, in initLPO4

root=root, outputfilename=outputfilename, cleanup=cleanup)

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 1019, in __init__

detect_bonds_between_cycles=detect_bonds_between_cycles)

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 779, in __init__

detectAll=self.detect_bonds_between_cycles)

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 1798, in __init__

self.__classifyBonds(molecule.allAtoms, allow_guanidinium_torsions)

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 1836, in __classifyBonds

dict =self.dict = ADBC.classify(mol.allAtoms.bonds[0])

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/AutoDockBondClassifier.py", line 58, in classify

rotatables = self.d['rotatable'].select(bonds)

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/MolKit/bondSelector.py", line 535, in select

rotatable = BondOrderBondSelector().select(bnds,1)

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/MolKit/bondSelector.py", line 508, in select

atype.assignHybridization(allAts)

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/PyBabel/atomTypes.py", line 137, in assignHybridization

self.valence_two()

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/PyBabel/atomTypes.py", line 266, in valence_two

angle1 = bond_angle(k.coords, a.coords, l.coords)

File "/home/garima/MGLTools-1.5.6/MGLToolsPckgs/PyBabel/util.py", line 47, in bond_angle

raise ZeroDivisionError("Input used:", a, b, c)

ZeroDivisionError: ('Input used:', [2.0, 0.0, 0.0], [2.0, 0.0, 0.0], [2.0, 0.0, 0.0])

Kindly provide me some ideas to overcome this problem.

Hi again,

AutoDock is also unable to handle metal ions as ligands. So you got those errors.

I suggest molecular dynamics simulations in place of molecular docking. Metal ion(s) should stay longer in region(s) that bind to them strongly.

http://ambermd.org/

Thanks Yoshinobu

Dear All

   I am using amber 14 for molecular dynamics simulation that was stopped without giving any error at 12 ns ,19 ns ,29 ns of different protein ligand complex . I can't understand what is the reason behind this .In Prod.info  file 0f 12ns is

NSTEP = 5783100 TIME(PS) = 12566.200 TEMP(K) = 300.70 PRESS = -407.9

Etot = -30562.5651 EKtot = 6624.5260 EPtot = -37187.0911

BOND = 235.2200 ANGLE = 552.9646 DIHED = 767.3419

1-4 NB = 231.3599 1-4 EEL = 4520.1681 VDWAALS = 6895.1572

EELEC = -50389.3028 EHBOND = 0.0000 RESTRAINT = 0.0000

EKCMT = 2911.0340 VIRIAL = 3844.8154 VOLUME = 106013.5791

Density = 1.0554

Ewald error estimate: 0.2098E-03

------------------------------------------------------------------------------

| Current Timing Info

| -------------------

| Total steps : 25000000 | Completed : 5783100 | Remaining : 19216900

|

| Average timings for last 100 steps:

| Elapsed(s) = 2.71 Per Step(ms) = 27.07

| ns/day = 6.38 seconds/ns = 13532.80

|

| Average timings for all steps:

| Elapsed(s) = 181035.03 Per Step(ms) = 31.30

| ns/day = 5.52 seconds/ns = 15652.08

|

| Estimated time remaining: 167.1 hours.

I want to know why the simulation is stop . I need to restart a molecular dynamics calculation  what should I do now? 

Thanks

Hi again,

The following Amber archive might help you:

http://archive.ambermd.org/200602/0281.html

Hi ,

I am not running this simulation via PBS. and when i restart same simulation using sander mpi it is again stop at

NSTEP = 5436400 TIME(PS) = 11872.800 TEMP(K) = 304.85 PRESS = 102.2

Etot = -30650.5478 EKtot = 6715.9220 EPtot = -37366.4699

BOND = 211.4945 ANGLE = 550.8857 DIHED = 748.7218

1-4 NB = 242.2749 1-4 EEL = 4485.1930 VDWAALS = 7176.5078

EELEC = -50781.5476 EHBOND = 0.0000 RESTRAINT = 0.0000

EKCMT = 2916.5980 VIRIAL = 2683.1241 VOLUME = 105849.5973

Density = 1.0570

Ewald error estimate: 0.4595E-03

------------------------------------------------------------------------------

| Current Timing Info

| -------------------

| Total steps : 25000000 | Completed : 5436400 | Remaining : 19563600

|

| Average timings for last 100 steps:

| Elapsed(s) = 2.71 Per Step(ms) = 27.14

| ns/day = 6.37 seconds/ns = 13568.33

|

| Average timings for all steps:

| Elapsed(s) = 148729.95 Per Step(ms) = 27.36

| ns/day = 6.32 seconds/ns = 13679.08

Every time it is stop in different ns of time while there is no change in min.in ,heat.in, prod.in input files. i want to know why simulation is stop different time period. while there is same script is used.what should i do now?

Hi,

You should check your initial structure, leap.log, and trajectories obtained so far.

I recommend you should visit the following links again, and post your question there:

http://ambermd.org/

http://ambermd.org/tutorials/basic/tutorial1/

http://ambermd.org/tutorials/advanced/tutorial3/