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.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@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.war...@monash.edu<mailto:dallas.war...@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.war...@monash.edu<mailto:dallas.war...@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-boun...@gromacs.org<mailto:gmx-users-boun...@gromacs.org> [mailto:gmx-users-boun...@gromacs.org<mailto:gmx-users-boun...@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 : monu46...@yahoo.com<mailto:monu46...@yahoo.com> -- gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-users@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 or send it to gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 : monu46...@yahoo.com<mailto:monu46...@yahoo.com>
-- gmx-users mailing list gmx-users@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 or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists