[gmx-users] Re: Increase in charge after adding the ligand

Dallas Warren Dallas.Warren at monash.edu
Tue Jun 21 04:38:16 CEST 2011 

Go back through your procedure, repeating it again, step by step.  Take note of number of atoms, charges etc as you go.  And answer the other questions I put to you previously.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of bharat gupta
Sent: Tuesday, 21 June 2011 12:31 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: Increase in charge after adding the ligand

I checked the .gro file , in that only 9 NA are mentioned.. also during the minimization step I am getting the following error:-

step 100: Water molecule starting at atom 85940 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  100, Dmax= 2.4e-01 nm, Epot= -4.86897e+06 Fmax= 2.60577e+06, atom= 85940
Step=  101, Dmax= 2.8e-01 nm, Epot= -4.88265e+06 Fmax= 1.03794e+05, atom= 3628

step 102: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  102, Dmax= 3.4e-01 nm, Epot=  7.97834e+06 Fmax= 1.57210e+09, atom= 3631
step 103: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  104, Dmax= 8.5e-02 nm, Epot= -4.90566e+06 Fmax= 2.85624e+05, atom= 3628
Step=  105, Dmax= 1.0e-01 nm, Epot= -4.91390e+06 Fmax= 1.97964e+05, atom= 3628

step 106: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  107, Dmax= 6.2e-02 nm, Epot= -4.92487e+06 Fmax= 6.32096e+04, atom= 362885
Step=  108, Dmax= 7.4e-02 nm, Epot= -4.95276e+06 Fmax= 4.18514e+04, atom= 3627
Step=  109, Dmax= 8.9e-02 nm, Epot= -4.98566e+06 Fmax= 1.91771e+05, atom= 3620
Step=  110, Dmax= 1.1e-01 nm, Epot= -5.00651e+06 Fmax= 1.56721e+05, atom= 3620
Step=  112, Dmax= 6.4e-02 nm, Epot= -5.01376e+06 Fmax= 1.25375e+05, atom= 3620
Step=  113, Dmax= 7.7e-02 nm, Epot= -5.02950e+06 Fmax= 5.35431e+04, atom= 3620
Step=  114, Dmax= 9.2e-02 nm, Epot= -5.04978e+06 Fmax= 2.03884e+05, atom= 3620
Step=  115, Dmax= 1.1e-01 nm, Epot= -5.07406e+06 Fmax= 6.55437e+04, atom= 3620
Step=  116, Dmax= 1.3e-01 nm, Epot= -5.10420e+06 Fmax= 4.48874e+05, atom= 3620
Step=  117, Dmax= 1.6e-01 nm, Epot= -5.11132e+06 Fmax= 1.89966e+05, atom= 3620

step 118: Water molecule starting at atom 213098 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  118, Dmax= 1.9e-01 nm, Epot= -5.12615e+06 Fmax= 2.25039e+05, atom= 3620

step 119: Water molecule starting at atom 252632 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 119: Water molecule starting at atom 212687 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step=  119, Dmax= 2.3e-01 nm, Epot= -5.15014e+06 Fmax= 1.78972e+07, atom= 212687
Step=  120, Dmax= 2.7e-01 nm, Epot= -5.15139e+06 Fmax= 9.55607e+04, atom= 3620

step 121: Water molecule starting at atom 171371 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  122, Dmax= 1.6e-01 nm, Epot= -5.16214e+06 Fmax= 3.02686e+05, atom= 3620
Step=  123, Dmax= 2.0e-01 nm, Epot= -5.18637e+06 Fmax= 1.61921e+05, atom= 3620
Step=  124, Dmax= 2.4e-01 nm, Epot= -5.21873e+06 Fmax= 7.51816e+04, atom= 3620

step 125: Water molecule starting at atom 213098 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  125, Dmax= 2.8e-01 nm, Epot= -5.13297e+06 Fmax= 1.02333e+08, atom= 212927
step 126: Water molecule starting at atom 212927 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  126, Dmax= 1.4e-01 nm, Epot= -5.23551e+06 Fmax= 2.01165e+05, atom= 3620
Step=  127, Dmax= 1.7e-01 nm, Epot= -5.25949e+06 Fmax= 9.03334e+04, atom= 3620
Step=  129, Dmax= 1.0e-01 nm, Epot= -5.27727e+06 Fmax= 1.03222e+05, atom= 3620
Step=  130, Dmax= 1.2e-01 nm, Epot= -5.29146e+06 Fmax= 1.41302e+05, atom= 3630
Step=  132, Dmax= 7.4e-02 nm, Epot= -5.30238e+06 Fmax= 7.19601e+04, atom= 3630
Step=  133, Dmax= 8.8e-02 nm, Epot= -5.32013e+06 Fmax= 5.75864e+04, atom= 3630
Step=  134, Dmax= 1.1e-01 nm, Epot= -5.33172e+06 Fmax= 1.98591e+05, atom= 3622
Step=  135, Dmax= 1.3e-01 nm, Epot= -5.34273e+06 Fmax= 1.20478e+05, atom= 3622
Step=  136, Dmax= 1.5e-01 nm, Epot= -5.36395e+06 Fmax= 7.56979e+04, atom= 3620
Step=  138, Dmax= 9.2e-02 nm, Epot= -5.37722e+06 Fmax= 7.34765e+04, atom= 3622
Step=  139, Dmax= 1.1e-01 nm, Epot= -5.38280e+06 Fmax= 2.57798e+05, atom= 3622
Step=  140, Dmax= 1.3e-01 nm, Epot= -5.39328e+06 Fmax= 5.13241e+05, atom= 3622

step 141: Water molecule starting at atom 171395 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  142, Dmax= 7.9e-02 nm, Epot= -5.40360e+06 Fmax= 5.65055e+04, atom= 362295
Step=  143, Dmax= 9.5e-02 nm, Epot= -5.42336e+06 Fmax= 6.92127e+04, atom= 3620
Step=  144, Dmax= 1.1e-01 nm, Epot= -5.42672e+06 Fmax= 3.08454e+05, atom= 3620
Step=  145, Dmax= 1.4e-01 nm, Epot= -5.44497e+06 Fmax= 8.28412e+04, atom= 3620
Step=  146, Dmax= 1.6e-01 nm, Epot= -5.45986e+06 Fmax= 1.68180e+05, atom= 3620
Step=  147, Dmax= 2.0e-01 nm, Epot= -5.47710e+06 Fmax= 6.39076e+04, atom= 3620
Step=  150, Dmax= 5.9e-02 nm, Epot= -5.49010e+06 Fmax= 7.14589e+04, atom= 3620
Step=  151, Dmax= 7.1e-02 nm, Epot= -5.50033e+06 Fmax= 6.50889e+04, atom= 3631
Step=  152, Dmax= 8.5e-02 nm, Epot= -5.51008e+06 Fmax= 9.01451e+04, atom= 3631
Step=  153, Dmax= 1.0e-01 nm, Epot= -5.51782e+06 Fmax= 1.14429e+05, atom= 3631
Step=  154, Dmax= 1.2e-01 nm, Epot= -5.52769e+06 Fmax= 1.10653e+05, atom= 3631
Step=  155, Dmax= 1.5e-01 nm, Epot= -5.53537e+06 Fmax= 8.81568e+04, atom= 3631
Step=  157, Dmax= 8.8e-02 nm, Epot= -5.54703e+06 Fmax= 1.72202e+05, atom= 3627
Step=  158, Dmax= 1.1e-01 nm, Epot= -5.55035e+06 Fmax= 5.92969e+05, atom= 3627
Step=  159, Dmax= 1.3e-01 nm, Epot= -5.55740e+06 Fmax= 9.21361e+04, atom= 3627
Step=  161, Dmax= 7.6e-02 nm, Epot= -5.56682e+06 Fmax= 4.70994e+04, atom= 3627
Step=  162, Dmax= 9.2e-02 nm, Epot= -5.58254e+06 Fmax= 4.61149e+04, atom= 3627
Step=  163, Dmax= 1.1e-01 nm, Epot= -5.58425e+06 Fmax= 2.41217e+05, atom= 3627
Step=  164, Dmax= 1.3e-01 nm, Epot= -5.60094e+06 Fmax= 1.54088e+05, atom= 3627
Step=  165, Dmax= 1.6e-01 nm, Epot= -5.60984e+06 Fmax= 1.35631e+05, atom= 3627
Step=  166, Dmax= 1.9e-01 nm, Epot= -5.62023e+06 Fmax= 8.55147e+04, atom= 3627
Step=  168, Dmax= 1.1e-01 nm, Epot= -5.63209e+06 Fmax= 8.17613e+04, atom= 3627
Step=  169, Dmax= 1.4e-01 nm, Epot= -5.64107e+06 Fmax= 8.85408e+04, atom= 3627
Step=  171, Dmax= 8.2e-02 nm, Epot= -5.65284e+06 Fmax= 5.15772e+04, atom= 3627
Step=  172, Dmax= 9.8e-02 nm, Epot= -5.65812e+06 Fmax= 1.01666e+05, atom= 3628
Step=  173, Dmax= 1.2e-01 nm, Epot= -5.66262e+06 Fmax= 1.88903e+05, atom= 3628
Step=  174, Dmax= 1.4e-01 nm, Epot= -5.67125e+06 Fmax= 1.44782e+05, atom= 3628

step 175: Water molecule starting at atom 86381 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  175, Dmax= 1.7e-01 nm, Epot= -5.67920e+06 Fmax= 2.18421e+05, atom= 86381
Step=  193, Dmax= 1.6e-06 nm, Epot= -5.66548e+06 Fmax= 4.55942e+05, atom= 125963
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 194 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -5.6791960e+06
Maximum force     =  2.1842059e+05 on atom 86381
Norm of force     =  5.6555481e+02

On Tue, Jun 21, 2011 at 11:10 AM, Dallas Warren <Dallas.Warren at monash.edu<mailto:Dallas.Warren at monash.edu>> wrote:
You need to work out exactly why you have the mis-match, something is screwy.

Something that you are doing does not add up.

What is the charge on the ligand?  Appears to be -7.

Why when you add 9 Na+ do you then end up with a charge of +8?  Seems that you have actually added 17 sodiums from those numbers.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu<mailto:dallas.warren at monash.edu>
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org<mailto:gmx-users-bounces at gromacs.org> [mailto:gmx-users-bounces at gromacs.org<mailto:gmx-users-bounces at gromacs.org>] On Behalf Of bharat gupta
Sent: Tuesday, 21 June 2011 12:05 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Re: Increase in charge after adding the ligand

Hi,

Initially while preparing the structure , -2 charge was there on the protein. Next, after adding the ligand and executing grompp statement It showing -9.9 charge. So I added 9 sodium ions. but still its showing +8 charge on the system. what shall I do in this case ??

--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com<mailto:monu46010 at yahoo.com>


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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com<mailto:monu46010 at yahoo.com>

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