hello,<br>I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command<br><br>
Fatal error:<br>Atomtype HW not found<br><br>can anyone provide me some help?<br><br>Thanx with anticipation.<br><br><br><div class="gmail_quote">On Fri, Nov 18, 2011 at 2:29 AM, Jose Tusell <span dir="ltr"><<a href="mailto:jrta1981@gmail.com">jrta1981@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">I'll try changing the step size first and if that fails I'll try<br>
another algorithm. Thanks for the input.<br>
<span class="HOEnZb"><font color="#888888"><br>
Jose Tusell<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
><br>
><br>
> Jose Tusell wrote:<br>
>><br>
>> Hi Justin,<br>
>><br>
>> Thanks for the input on why this is happening. It sounds a little<br>
>> suspicious that the energy doesn't change after a few steps of energy<br>
>> minimization. Do you know of any way that I can find out what is<br>
>> going on?<br>
>><br>
><br>
> The screen output should indicate the atom with maximal force. Sometimes<br>
> the EM algorithms get stuck when the geometry cannot change without making<br>
> detrimental moves. You either need a larger step size, a different<br>
> algorithm, or a better starting structure, if that is the case. I have seen<br>
> this many times before, nothing suspicious about it.<br>
><br>
> -Justin<br>
><br>
>> Thanks,<br>
>><br>
>> Jose Tusell<br>
>><br>
>> On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
>> wrote:<br>
>>><br>
>>> Jose Tusell wrote:<br>
>>>><br>
>>>> Hi Cristoph,<br>
>>>><br>
>>>> Thanks for the reply. I found that my problem was not gromacs. The<br>
>>>> input that ORCA was receiving from GROMACS did not have the correct<br>
>>>> number of hydrogens. I've solved this problem now and ORCA is running<br>
>>>> fine. I however ran into another problem with my energy minimization.<br>
>>>> The output from my gromacs log file is the following:<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 0 0.00000 0.00000<br>
>>>><br>
>>>> Energies (kJ/mol)<br>
>>>> Bond Angle Proper Dih. Improper Dih.<br>
>>>> LJ-14<br>
>>>> 1.21899e+04 1.92496e+03 5.62567e+03 1.49141e+01<br>
>>>> 3.68001e+03<br>
>>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum<br>
>>>> En.<br>
>>>> 2.41200e+04 1.47494e+05 -5.06544e+05 -7.56009e+04<br>
>>>> -3.96508e+06<br>
>>>> Potential Pressure (bar)<br>
>>>> -4.35218e+06 -2.10629e+04<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 1 1.00000 0.00000<br>
>>>><br>
>>>> Energies (kJ/mol)<br>
>>>> Bond Angle Proper Dih. Improper Dih.<br>
>>>> LJ-14<br>
>>>> 1.20006e+04 1.92297e+03 5.62600e+03 1.47801e+01<br>
>>>> 3.67746e+03<br>
>>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum<br>
>>>> En.<br>
>>>> 2.41174e+04 1.46421e+05 -5.06609e+05 -7.56156e+04<br>
>>>> -4.00402e+06<br>
>>>> Potential Pressure (bar)<br>
>>>> -4.39246e+06 -2.10739e+04<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 2 2.00000 0.00000<br>
>>>><br>
>>>> Energies (kJ/mol)<br>
>>>> Bond Angle Proper Dih. Improper Dih.<br>
>>>> LJ-14<br>
>>>> 1.17961e+04 1.92126e+03 5.62633e+03 1.46477e+01<br>
>>>> 3.67461e+03<br>
>>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum<br>
>>>> En.<br>
>>>> 2.41145e+04 1.45528e+05 -5.06679e+05 -7.56315e+04<br>
>>>> -4.18671e+06<br>
>>>> Potential Pressure (bar)<br>
>>>> -4.57635e+06 -2.10854e+04<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 3 3.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 4 4.00000 0.00000<br>
>>>><br>
>>>> Energies (kJ/mol)<br>
>>>> Bond Angle Proper Dih. Improper Dih.<br>
>>>> LJ-14<br>
>>>> 1.16705e+04 1.92041e+03 5.62652e+03 1.45728e+01<br>
>>>> 3.67282e+03<br>
>>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum<br>
>>>> En.<br>
>>>> 2.41128e+04 1.45113e+05 -5.06721e+05 -7.56410e+04<br>
>>>> -4.24486e+06<br>
>>>> Potential Pressure (bar)<br>
>>>> -4.63509e+06 -2.10913e+04<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 5 5.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 6 6.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 7 7.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 8 8.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 9 9.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 10 10.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 11 11.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 12 12.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 13 13.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 14 14.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 15 15.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 16 16.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 17 17.00000 0.00000<br>
>>>><br>
>>>> Step Time Lambda<br>
>>>> 18 18.00000 0.00000<br>
>>>><br>
>>>><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>
>>>> Why doesn't GROMACS output the energies for certain steps? Step 3 and<br>
>>>> steps 5-18 do show any output in the log file. Any ideas why this is<br>
>>>> happening?<br>
>>>><br>
>>> This happens for the reasons printed by mdrun - those steps caused no<br>
>>> change<br>
>>> in energy.<br>
>>><br>
>>> -Justin<br>
>>><br>
>>> --<br>
>>> ========================================<br>
>>><br>
>>> Justin A. Lemkul<br>
>>> Ph.D. Candidate<br>
>>> ICTAS Doctoral Scholar<br>
>>> MILES-IGERT Trainee<br>
>>> Department of Biochemistry<br>
>>> Virginia Tech<br>
>>> Blacksburg, VA<br>
>>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
>>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>>><br>
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>>><br>
>><br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
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</div></div></blockquote></div><br>