<div dir="ltr"><div>Dear Chimera dev. team,<br><br><br></div><div>I have to use my own set of Amber99 parameters because I'm working with transition metals. I'm testing if I can minimize a benchmark system that contains one copper atom coordinated to 6 water molecules. To do it, I don't use any script, I use directly the tool "minimize" present in Tools-> Structure Editing.<br>
<br>To do so I edited the frcmod.ff99SB file with the atom, bond, dihedral... all the fields that frcmod.ff99SB ask to me. That didn't work (Element "Cu" is not currently supported by MMTK). Then I followed the instructions here:<br>
<br><a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations</a><br>
<br></div><div>and I put a file called "cu" with the required data in: lib/python*/site-packages/MMTK/Database/Atoms<br>
<br></div><div>I tried again, and the same problem.<br></div><div><br></div><div>In the same webpage, there are instructions of how can we edit the Amber parameters files present in: bin/amber11/dat/leap/parm<br></div><div>
I put my parameters in frcmod.ff99SB and I also tried to put it in frcmod.ff03, but it fails again.<br><br></div><div>How can I solve this problem and perform the minimizations? <br></div><div><br></div><div>I'm using both windows(x64) and linux(x86) versions of Chimera 1.6.2 (build 36855) but I planned to finish the testing with Chimera 1.7 that contains by default the Amber12 package.<br>
</div><div>At the bottom of the message there is the mol2 file and the parameters that I'm testing.<br></div><div><br></div><div>Thanks in advance for your time.<br></div><div><br>Elisabeth O.-C.<br></div><div><br><br>
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My mol2 file is:<br><br></div><div>@<TRIPOS>MOLECULE<br>cuh2o.mol2<br>19 12 1 0 0<br>SMALL<br>AMBER ff99SB<br><br><br>@<TRIPOS>ATOM<br> 1 CU 0.0581 0.0224 0.0049 CU 1 UNK 2.0000<br>
2 OH -2.2040 0.0438 0.0019 O.3 1 UNK -0.8230<br> 3 OH -0.0067 -0.2388 2.1919 O.3 1 UNK -0.8370<br> 4 OH 0.0041 0.2849 -2.1820 O.3 1 UNK -0.8450<br>
5 OH 2.2006 0.0021 0.0073 O.3 1 UNK -0.8270<br> 6 OH -0.0248 -2.4186 -0.2871 O.3 1 UNK -0.8330<br> 7 OH 0.0202 2.4645 0.2971 O.3 1 UNK -0.8420<br>
8 H15 -2.6953 -0.0699 0.6640 H 1 UNK 0.4010<br> 9 H16 -0.6665 -0.1584 2.6929 H 1 UNK 0.4170<br> 10 H18 -0.6618 0.2534 -2.6804 H 1 UNK 0.4330<br>
11 H19 2.6899 -0.0779 -0.6612 H 1 UNK 0.4240<br> 12 H20 0.6422 -2.9163 -0.2996 H 1 UNK 0.4180<br> 13 H14 0.6417 2.9769 0.0874 H 1 UNK 0.4200<br>
14 H17 -2.6936 -0.1186 -0.6513 H 1 UNK 0.4180<br> 15 H22 0.6497 -0.1530 2.6964 H 1 UNK 0.4220<br> 16 H21 0.6504 0.1511 -2.6890 H 1 UNK 0.4130<br>
17 H13 2.6872 -0.2103 0.6483 H 1 UNK 0.4060<br> 18 H24 -0.6602 -2.9263 -0.1105 H 1 UNK 0.4160<br> 19 H23 -0.6488 2.9572 0.3459 H 1 UNK 0.4200<br>
@<TRIPOS>BOND<br> 1 18 6 1<br> 2 14 2 1<br> 3 10 4 1<br> 4 9 3 1<br> 5 8 2 1<br> 6 19 7 1<br> 7 6 12 1<br> 8 17 5 1<br> 9 16 4 1<br>
10 15 3 1<br> 11 13 7 1<br> 12 5 11 1<br>@<TRIPOS>SUBSTRUCTURE<br> 1 UNK 1 RESIDUE 4 A UNK 0 ROOT<br><br><br></div><div>And my initial trial of parameters that I write in the mod file is (I put the same than Fe atom parameters written in the file frcmod.heme_ff94 only to test if that works):<br>
<br></div><div>MASS<br></div><div>CU 63.55<br><br></div><div>BOND<br></div><div>CU-OH 200.00 2.0<br><br></div><div>ANGLE<br></div><div>CU-OH-HO 35.00 120.00<br></div><div>OH-CU-OH 50.00 90.00<br></div><div><br></div><div>
DIHEDAL<br></div><div>X-OH-CU-X 1 0.00 0.00 2.0<br><br></div><div>NONBON<br></div><div>CU 1.2 0.05 0.00<br></div><div><br></div><div><br></div>-- <br><font><span style="font-family:trebuchet ms,sans-serif">Elisabeth Ortega Carrasco, Ph.D. Student</span><br style="font-family:trebuchet ms,sans-serif">
<span style="font-family:trebuchet ms,sans-serif">
Molecular Modelling of Transition Metal Systems Group</span><br style="font-family:trebuchet ms,sans-serif"><span style="font-family:trebuchet ms,sans-serif">
Lab. C7/153, Chemistry Department</span><br style="font-family:trebuchet ms,sans-serif"><span style="font-family:trebuchet ms,sans-serif">
Universitat Autonoma de Barcelona</span><br style="font-family:trebuchet ms,sans-serif"><br style="font-family:trebuchet ms,sans-serif"><span style="font-family:trebuchet ms,sans-serif">
Tel.: <a href="tel:%2B34935812857" value="+34935812857" target="_blank">+34935812857</a></span></font>
<font><br style="font-family:trebuchet ms,sans-serif"><span style="font-family:trebuchet ms,sans-serif">
email.: </span><a style="font-family:trebuchet ms,sans-serif" href="mailto:ortega.elisabeth@qf.uab.cat" target="_blank">ortega.elisabeth@qf.uab.cat</a></font>
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