(unknown charset) Re: [AMBER] Metal center molecule

From: (unknown charset) 高含露 <gaohanlu95.163.com>
Date: Wed, 16 Jan 2019 11:41:47 +0800 (CST)

Dear Saikat Pal,
  Thanks for your reply! I'v tried to set different box volume, but the minimization always fails. And I still can't use pmemd to do the minimization. The min.out file can be seen in attachment. I would really appreciate your help!


Hanlu Gao




At 2019-01-15 21:24:23, "Saikat Pal" <saikatpaliitg.yahoo.com> wrote:
>Dear Hanlu Gao,Have you tried with different box volume? Maybe box volume should be increased.
>
>Thanks and Regards,
>Saikat Pal
>
>
>
>
>
> On Tuesday, 15 January, 2019, 8:52:39 AM IST, gaohanlu <gaohanlu95.163.com> wrote:
>
> Dear All,
>
> I want to construct a small metal center molecule which is similar to cisplatin. The structure of the Pt complexes can be seen in attachment. I successfully build the molecule following the tutorial 20. The details is shown in attachment.
>Here is the mcpbpy.pdb I generated
>REMARK, BUILD BY MCPB.PY
>HETATM 1 C1 AD1 A 1 -10.711 2.606 -0.195 1.00 0.00
>HETATM 2 C2 AD1 A 1 -9.402 2.706 -0.124 1.00 0.00
>HETATM 3 C3 AD1 A 1 -8.556 1.526 -0.055 1.00 0.00
>HETATM 4 C4 AD1 A 1 -9.145 0.322 -0.068 1.00 0.00
>HETATM 5 C5 AD1 A 1 -10.629 0.274 -0.147 1.00 0.00
>HETATM 6 C6 AD1 A 1 -11.351 1.378 -0.207 1.00 0.00
>HETATM 7 C7 AD1 A 1 -12.812 1.167 -0.289 1.00 0.00
>HETATM 8 O8 AD1 A 1 -13.083 -0.036 -0.259 1.00 0.00
>HETATM 9 O9 AD1 A 1 -13.936 2.068 -0.449 1.00 0.00
>HETATM 10 C27 AD1 A 1 -7.091 1.781 0.036 1.00 0.00
>HETATM 11 N28 AD1 A 1 -6.771 3.017 0.107 1.00 0.00
>HETATM 12 N29 AD1 A 1 -5.525 3.532 0.233 1.00 0.00
>HETATM 13 C30 AD1 A 1 -4.357 2.761 0.155 1.00 0.00
>HETATM 14 O31 AD1 A 1 -4.428 1.539 -0.067 1.00 0.00
>HETATM 15 C32 AD1 A 1 -3.022 3.391 0.445 1.00 0.00
>HETATM 16 N33 AD1 A 1 -2.842 4.628 0.778 1.00 0.00
>HETATM 17 N34 AD1 A 1 -1.480 4.859 1.023 1.00 0.00
>HETATM 18 C35 AD1 A 1 -0.780 3.655 0.811 1.00 0.00
>HETATM 19 C36 AD1 A 1 -1.724 2.712 0.443 1.00 0.00
>HETATM 20 C37 AD1 A 1 -1.411 1.449 0.170 1.00 0.00
>HETATM 21 C38 AD1 A 1 0.034 1.062 0.272 1.00 0.00
>HETATM 22 C39 AD1 A 1 0.942 1.983 0.633 1.00 0.00
>HETATM 23 C40 AD1 A 1 0.519 3.371 0.926 1.00 0.00
>HETATM 24 C41 AD1 A 1 -0.940 6.110 1.594 1.00 0.00
>HETATM 25 C42 AD1 A 1 -0.670 7.131 0.507 1.00 0.00
>HETATM 26 C43 AD1 A 1 -1.245 8.337 0.545 1.00 0.00
>HETATM 27 C44 AD1 A 1 -0.964 9.321 -0.499 1.00 0.00
>HETATM 28 C45 AD1 A 1 -0.116 9.024 -1.489 1.00 0.00
>HETATM 29 C46 AD1 A 1 0.527 7.698 -1.517 1.00 0.00
>HETATM 30 C47 AD1 A 1 0.253 6.809 -0.570 1.00 0.00
>HETATM 31 CL48 AD1 A 1 1.649 7.269 -2.764 1.00 0.00
>HETATM 32 CL49 AD1 A 1 -1.735 10.863 -0.426 1.00 0.00
>HETATM 33 H1 AD1 A 1 -11.309 3.488 -0.243 1.00 0.00
>HETATM 34 H2 AD1 A 1 -8.984 3.644 -0.119 1.00 0.00
>HETATM 35 H3 AD1 A 1 -8.582 -0.588 -0.017 1.00 0.00
>HETATM 36 H4 AD1 A 1 -11.149 -0.632 -0.162 1.00 0.00
>HETATM 37 H29 AD1 A 1 -6.336 0.985 0.071 1.00 0.00
>HETATM 38 H30 AD1 A 1 -5.436 4.506 0.404 1.00 0.00
>HETATM 39 H31 AD1 A 1 -2.165 0.739 -0.109 1.00 0.00
>HETATM 40 H32 AD1 A 1 0.353 0.058 0.064 1.00 0.00
>HETATM 41 H33 AD1 A 1 1.966 1.714 0.709 1.00 0.00
>HETATM 42 H34 AD1 A 1 1.244 4.108 1.217 1.00 0.00
>HETATM 43 H35 AD1 A 1 -1.655 6.542 2.316 1.00 0.00
>HETATM 44 H36 AD1 A 1 0.030 5.868 2.071 1.00 0.00
>HETATM 45 H37 AD1 A 1 -1.903 8.599 1.334 1.00 0.00
>HETATM 46 H38 AD1 A 1 0.096 9.743 -2.251 1.00 0.00
>HETATM 47 H39 AD1 A 1 0.715 5.872 -0.595 1.00 0.00
>TER
>HETATM 48 PT PT1 A 2 -13.906 4.071 -0.556 1.00 0.00
>TER
>HETATM 49 N11 ND1 A 3 -12.352 4.119 -1.833 1.00 0.00
>HETATM 50 H12 ND1 A 3 -12.100 3.178 -2.104 1.00 0.00
>HETATM 51 H13 ND1 A 3 -12.645 4.620 -2.673 1.00 0.00
>HETATM 52 H14 ND1 A 3 -11.558 4.612 -1.412 1.00 0.00
>TER
>HETATM 53 N15 N31 A 4 -12.637 4.128 1.076 1.00 0.00
>HETATM 54 H16 N31 A 4 -12.412 3.189 1.376 1.00 0.00
>HETATM 55 H17 N31 A 4 -11.789 4.660 0.845 1.00 0.00
>HETATM 56 H18 N31 A 4 -13.102 4.573 1.858 1.00 0.00
>TER
>HETATM 57 CL C11 A 5 -15.701 4.015 0.913 1.00 0.00
>TER
>HETATM 58 CL C21 A 6 -15.320 4.006 -2.372 1.00 0.00
>TER
>HETATM 59 O21 CD1 A 7 -13.875 6.061 -0.664 1.00 0.00
>HETATM 60 C22 CD1 A 7 -14.052 6.697 0.531 1.00 0.00
>HETATM 61 O23 CD1 A 7 -14.325 6.016 1.519 1.00 0.00
>HETATM 62 N24 CD1 A 7 -13.848 8.024 0.597 1.00 0.00
>HETATM 63 C25 CD1 A 7 -13.450 8.710 -0.585 1.00 0.00
>HETATM 64 C26 CD1 A 7 -11.953 8.387 -0.857 1.00 0.00
>HETATM 65 H23 CD1 A 7 -13.915 8.476 1.436 1.00 0.00
>HETATM 66 H24 CD1 A 7 -14.039 8.336 -1.432 1.00 0.00
>HETATM 67 H25 CD1 A 7 -13.579 9.791 -0.461 1.00 0.00
>HETATM 68 H26 CD1 A 7 -11.632 8.887 -1.767 1.00 0.00
>HETATM 69 H27 CD1 A 7 -11.824 7.292 -0.981 1.00 0.00
>HETATM 70 H28 CD1 A 7 -11.341 8.734 -0.012 1.00 0.00
>END
>
>For the current problem, I cant do the MD simulation. I use pmemd to do minimization, there is a error reported in min.out file like this,
>Error : Pmemd does not support single H residues!
>Then I use sander to do minimization, the system looks like crush down. It seems like the energy is too high to crush down.
>
>NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 -1.6686E+09 8.5270E+13 3.1275E+15 CL 58
>
> BOND = 257.6294 ANGLE = 132.6428 DIHED = 7.5868
> VDWAALS = 773.1926 EEL = ************* HBOND = 0.0000
> 1-4 VDW = 21.9709 1-4 EEL = -1073.9743 RESTRAINT = 0.0000
>
>Your suggestions and tips are highly appreciate,
>Thanks in advance!
>
>Beat regard!
>
>Hanlu Gao
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Received on Tue Jan 15 2019 - 20:00:02 PST
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