Bad angles not being removed?

[lvotapka]

In line 154 of run_qmmmrebind_trypsin_benzamidine.py, the remove_bad_angle_params() function is called. This function appears to open "guest_qm_params.txt" and detects lines between "Begin writing the Angle Parameters" and "Finish writing the Angle Parameters". In the file guest_qm_params.txt, those lines don't seem to exist. Is this a problem?

[anandojha]

Yes, this seems to be a problem. In the host-guest system, guest_qm_params.txt looks like the following: Begin writing the Bond Parameters

                            <Bond d="0.1104" k="134795.928" p1="147" p2="149"/>
                            <Bond d="0.11" k="139427.616" p1="147" p2="150"/>
                            <Bond d="0.153" k="88826.32" p1="147" p2="151"/>
                            <Bond d="0.1104" k="133197.64" p1="151" p2="152"/>
                            <Bond d="0.1104" k="133226.928" p1="151" p2="153"/>
                            <Bond d="0.1523" k="91227.936" p1="151" p2="154"/>
                            <Bond d="0.111" k="126423.744" p1="154" p2="155"/>
                            <Bond d="0.1109" k="128088.976" p1="154" p2="156"/>
                            <Bond d="0.1424" k="104712.968" p1="154" p2="157"/>
                            <Bond d="0.09667" k="223513.464" p1="157" p2="158"/>

Finish writing the Bond Parameters Begin writing the Angle Parameters

                            <Angle a="1.891937" k="157.23472" p1="148" p2="147" p3="150"/>
                            <Angle a="1.944297" k="174.01256" p1="148" p2="147" p3="151"/>
                            <Angle a="1.87972" k="134.39008" p1="149" p2="147" p3="150"/>
                            <Angle a="1.940806" k="282.04344" p1="149" p2="147" p3="151"/>
                            <Angle a="1.926843" k="191.92008" p1="150" p2="147" p3="151"/>
                            <Angle a="1.918117" k="59.66384" p1="147" p2="151" p3="152"/>
                            <Angle a="1.928589" k="223.50928" p1="147" p2="151" p3="153"/>
                            <Angle a="1.975713" k="437.6464" p1="147" p2="151" p3="154"/>
                            <Angle a="1.862266" k="167.90392" p1="152" p2="151" p3="153"/>
                            <Angle a="1.884956" k="232.46304" p1="152" p2="151" p3="154"/>
                            <Angle a="1.890192" k="206.6896" p1="153" p2="151" p3="154"/>
                            <Angle a="1.912881" k="275.60008" p1="151" p2="154" p3="155"/>
                            <Angle a="1.914626" k="252.96464" p1="151" p2="154" p3="156"/>
                            <Angle a="1.886701" k="437.228" p1="151" p2="154" p3="157"/>
                            <Angle a="1.872738" k="163.05048" p1="155" p2="154" p3="156"/>
                            <Angle a="1.939061" k="221.20808" p1="155" p2="154" p3="157"/>
                            <Angle a="1.939061" k="206.64776" p1="156" p2="154" p3="157"/>
                            <Angle a="1.884956" k="283.13128" p1="154" p2="157" p3="158"/>

Finish writing the Angle Parameters Begin writing the Charge Parameters

Finish writing the Charge Parameters

It means the angle parameters are not recorded in one of the steps.

[lvotapka]

OK glad we caught that.

[anandojha]

I will have to look deeper and see why the angle parameters are not being recorded for the trypsin -benzamidine case but it is good for all the other cases. I will look into this by today.

[anandojha]

BTW, this means that the prmtop file will contain the QM-parameters for the charge, bond, and torsions but the angles will be present for the non-QM parameters.

[lvotapka]

I wonder if that's why aspirin was blowing up.

[anandojha]

I introduced this function to check for the bad angles in the case of aspirin, so this is a glitch in the front end for the trypsin-benzamidine systems. As far as aspirin is concerned, the aspirin molecule becomes more flexible as a consequence of new parameters and comes too close to the host in the first anchor. If we define the bound state a bit far aware from the host or change the orientation slightly, aspirin works.

[anandojha]

In the aspirin files, the paramaters do appear for the angles.