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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>bharat gupta<br>
<b>Sent:</b> Tuesday, 21 June 2011 12:31 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] Re: Increase in charge after adding the ligand<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">I checked the .gro file , in that only 9 NA are mentioned.. also during the minimization step I am getting the following error:-<br>
<br>
step 100: Water molecule starting at atom 85940 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Step= 100, Dmax= 2.4e-01 nm, Epot= -4.86897e+06 Fmax= 2.60577e+06, atom= 85940<br>
Step= 101, Dmax= 2.8e-01 nm, Epot= -4.88265e+06 Fmax= 1.03794e+05, atom= 3628<br>
<br>
step 102: Water molecule starting at atom 125885 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Step= 102, Dmax= 3.4e-01 nm, Epot= 7.97834e+06 Fmax= 1.57210e+09, atom= 3631<br>
step 103: Water molecule starting at atom 125885 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Step= 104, Dmax= 8.5e-02 nm, Epot= -4.90566e+06 Fmax= 2.85624e+05, atom= 3628<br>
Step= 105, Dmax= 1.0e-01 nm, Epot= -4.91390e+06 Fmax= 1.97964e+05, atom= 3628<br>
<br>
step 106: Water molecule starting at atom 125885 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Step= 107, Dmax= 6.2e-02 nm, Epot= -4.92487e+06 Fmax= 6.32096e+04, atom= 362885<br>
Step= 108, Dmax= 7.4e-02 nm, Epot= -4.95276e+06 Fmax= 4.18514e+04, atom= 3627<br>
Step= 109, Dmax= 8.9e-02 nm, Epot= -4.98566e+06 Fmax= 1.91771e+05, atom= 3620<br>
Step= 110, Dmax= 1.1e-01 nm, Epot= -5.00651e+06 Fmax= 1.56721e+05, atom= 3620<br>
Step= 112, Dmax= 6.4e-02 nm, Epot= -5.01376e+06 Fmax= 1.25375e+05, atom= 3620<br>
Step= 113, Dmax= 7.7e-02 nm, Epot= -5.02950e+06 Fmax= 5.35431e+04, atom= 3620<br>
Step= 114, Dmax= 9.2e-02 nm, Epot= -5.04978e+06 Fmax= 2.03884e+05, atom= 3620<br>
Step= 115, Dmax= 1.1e-01 nm, Epot= -5.07406e+06 Fmax= 6.55437e+04, atom= 3620<br>
Step= 116, Dmax= 1.3e-01 nm, Epot= -5.10420e+06 Fmax= 4.48874e+05, atom= 3620<br>
Step= 117, Dmax= 1.6e-01 nm, Epot= -5.11132e+06 Fmax= 1.89966e+05, atom= 3620<br>
<br>
step 118: Water molecule starting at atom 213098 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Step= 118, Dmax= 1.9e-01 nm, Epot= -5.12615e+06 Fmax= 2.25039e+05, atom= 3620<br>
<br>
step 119: Water molecule starting at atom 252632 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
<br>
step 119: Water molecule starting at atom 212687 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>
Step= 119, Dmax= 2.3e-01 nm, Epot= -5.15014e+06 Fmax= 1.78972e+07, atom= 212687<br>
Step= 120, Dmax= 2.7e-01 nm, Epot= -5.15139e+06 Fmax= 9.55607e+04, atom= 3620<br>
<br>
step 121: Water molecule starting at atom 171371 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Step= 122, Dmax= 1.6e-01 nm, Epot= -5.16214e+06 Fmax= 3.02686e+05, atom= 3620<br>
Step= 123, Dmax= 2.0e-01 nm, Epot= -5.18637e+06 Fmax= 1.61921e+05, atom= 3620<br>
Step= 124, Dmax= 2.4e-01 nm, Epot= -5.21873e+06 Fmax= 7.51816e+04, atom= 3620<br>
<br>
step 125: Water molecule starting at atom 213098 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Step= 125, Dmax= 2.8e-01 nm, Epot= -5.13297e+06 Fmax= 1.02333e+08, atom= 212927<br>
step 126: Water molecule starting at atom 212927 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Step= 126, Dmax= 1.4e-01 nm, Epot= -5.23551e+06 Fmax= 2.01165e+05, atom= 3620<br>
Step= 127, Dmax= 1.7e-01 nm, Epot= -5.25949e+06 Fmax= 9.03334e+04, atom= 3620<br>
Step= 129, Dmax= 1.0e-01 nm, Epot= -5.27727e+06 Fmax= 1.03222e+05, atom= 3620<br>
Step= 130, Dmax= 1.2e-01 nm, Epot= -5.29146e+06 Fmax= 1.41302e+05, atom= 3630<br>
Step= 132, Dmax= 7.4e-02 nm, Epot= -5.30238e+06 Fmax= 7.19601e+04, atom= 3630<br>
Step= 133, Dmax= 8.8e-02 nm, Epot= -5.32013e+06 Fmax= 5.75864e+04, atom= 3630<br>
Step= 134, Dmax= 1.1e-01 nm, Epot= -5.33172e+06 Fmax= 1.98591e+05, atom= 3622<br>
Step= 135, Dmax= 1.3e-01 nm, Epot= -5.34273e+06 Fmax= 1.20478e+05, atom= 3622<br>
Step= 136, Dmax= 1.5e-01 nm, Epot= -5.36395e+06 Fmax= 7.56979e+04, atom= 3620<br>
Step= 138, Dmax= 9.2e-02 nm, Epot= -5.37722e+06 Fmax= 7.34765e+04, atom= 3622<br>
Step= 139, Dmax= 1.1e-01 nm, Epot= -5.38280e+06 Fmax= 2.57798e+05, atom= 3622<br>
Step= 140, Dmax= 1.3e-01 nm, Epot= -5.39328e+06 Fmax= 5.13241e+05, atom= 3622<br>
<br>
step 141: Water molecule starting at atom 171395 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Step= 142, Dmax= 7.9e-02 nm, Epot= -5.40360e+06 Fmax= 5.65055e+04, atom= 362295<br>
Step= 143, Dmax= 9.5e-02 nm, Epot= -5.42336e+06 Fmax= 6.92127e+04, atom= 3620<br>
Step= 144, Dmax= 1.1e-01 nm, Epot= -5.42672e+06 Fmax= 3.08454e+05, atom= 3620<br>
Step= 145, Dmax= 1.4e-01 nm, Epot= -5.44497e+06 Fmax= 8.28412e+04, atom= 3620<br>
Step= 146, Dmax= 1.6e-01 nm, Epot= -5.45986e+06 Fmax= 1.68180e+05, atom= 3620<br>
Step= 147, Dmax= 2.0e-01 nm, Epot= -5.47710e+06 Fmax= 6.39076e+04, atom= 3620<br>
Step= 150, Dmax= 5.9e-02 nm, Epot= -5.49010e+06 Fmax= 7.14589e+04, atom= 3620<br>
Step= 151, Dmax= 7.1e-02 nm, Epot= -5.50033e+06 Fmax= 6.50889e+04, atom= 3631<br>
Step= 152, Dmax= 8.5e-02 nm, Epot= -5.51008e+06 Fmax= 9.01451e+04, atom= 3631<br>
Step= 153, Dmax= 1.0e-01 nm, Epot= -5.51782e+06 Fmax= 1.14429e+05, atom= 3631<br>
Step= 154, Dmax= 1.2e-01 nm, Epot= -5.52769e+06 Fmax= 1.10653e+05, atom= 3631<br>
Step= 155, Dmax= 1.5e-01 nm, Epot= -5.53537e+06 Fmax= 8.81568e+04, atom= 3631<br>
Step= 157, Dmax= 8.8e-02 nm, Epot= -5.54703e+06 Fmax= 1.72202e+05, atom= 3627<br>
Step= 158, Dmax= 1.1e-01 nm, Epot= -5.55035e+06 Fmax= 5.92969e+05, atom= 3627<br>
Step= 159, Dmax= 1.3e-01 nm, Epot= -5.55740e+06 Fmax= 9.21361e+04, atom= 3627<br>
Step= 161, Dmax= 7.6e-02 nm, Epot= -5.56682e+06 Fmax= 4.70994e+04, atom= 3627<br>
Step= 162, Dmax= 9.2e-02 nm, Epot= -5.58254e+06 Fmax= 4.61149e+04, atom= 3627<br>
Step= 163, Dmax= 1.1e-01 nm, Epot= -5.58425e+06 Fmax= 2.41217e+05, atom= 3627<br>
Step= 164, Dmax= 1.3e-01 nm, Epot= -5.60094e+06 Fmax= 1.54088e+05, atom= 3627<br>
Step= 165, Dmax= 1.6e-01 nm, Epot= -5.60984e+06 Fmax= 1.35631e+05, atom= 3627<br>
Step= 166, Dmax= 1.9e-01 nm, Epot= -5.62023e+06 Fmax= 8.55147e+04, atom= 3627<br>
Step= 168, Dmax= 1.1e-01 nm, Epot= -5.63209e+06 Fmax= 8.17613e+04, atom= 3627<br>
Step= 169, Dmax= 1.4e-01 nm, Epot= -5.64107e+06 Fmax= 8.85408e+04, atom= 3627<br>
Step= 171, Dmax= 8.2e-02 nm, Epot= -5.65284e+06 Fmax= 5.15772e+04, atom= 3627<br>
Step= 172, Dmax= 9.8e-02 nm, Epot= -5.65812e+06 Fmax= 1.01666e+05, atom= 3628<br>
Step= 173, Dmax= 1.2e-01 nm, Epot= -5.66262e+06 Fmax= 1.88903e+05, atom= 3628<br>
Step= 174, Dmax= 1.4e-01 nm, Epot= -5.67125e+06 Fmax= 1.44782e+05, atom= 3628<br>
<br>
step 175: Water molecule starting at atom 86381 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Step= 175, Dmax= 1.7e-01 nm, Epot= -5.67920e+06 Fmax= 2.18421e+05, atom= 86381<br>
Step= 193, Dmax= 1.6e-06 nm, Epot= -5.66548e+06 Fmax= 4.55942e+05, atom= 125963<br>
Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 1000<br>
<br>
Double precision normally gives you higher accuracy.<br>
You might need to increase your constraint accuracy, or turn<br>
off constraints alltogether (set constraints = none in mdp file)<br>
<br>
writing lowest energy coordinates.<br>
<br>
Steepest Descents converged to machine precision in 194 steps,<br>
but did not reach the requested Fmax < 1000.<br>
Potential Energy = -5.6791960e+06<br>
Maximum force = 2.1842059e+05 on atom 86381<br>
Norm of force = 5.6555481e+02<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On Tue, Jun 21, 2011 at 11:10 AM, Dallas Warren <<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;color:#1F497D">You need to work out exactly why you have the mis-match, something is screwy.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;color:#1F497D">Something that you are doing does not add up.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;color:#1F497D">What is the charge on the ligand? Appears to be -7.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;color:#1F497D">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.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;color:#1F497D">Medicinal Chemistry and Drug Action</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;color:#1F497D">Monash Institute of Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;color:#1F497D">
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt">From:</span></b><span style="font-size:10.0pt">
<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>]
<b>On Behalf Of </b>bharat gupta<br>
<b>Sent:</b> Tuesday, 21 June 2011 12:05 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] Re: Increase in charge after adding the ligand</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi,<br>
<br>
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 ??<br clear="all">
<br>
-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Mobile no. - 010-5818-3680<br>
E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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--<br>
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<p class="MsoNormal"><br>
<br clear="all">
<br>
-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343<o:p></o:p></p>
<div>
<p class="MsoNormal">Mobile no. - 010-5818-3680<br>
E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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