On Thu, Jun 27, 2019 at 4:16 AM Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> Dear All,
> I tried the cpptraj checkstructure command, but it doesn't print anything
> in the reportfile.generated file (min-structure.txt, the file is empty).
All of the bad contact distances reported by leap are > 0.8 Ang, which
is the default cutoff for bad contacts in cpptraj. Try using 'cut 1.5'
or something.
-Dan
> My cpptraj commands are given below. This re-minimized the system shows
> two additional close contacts using the rst7 --> pdb --> leap flow.
> Can you please suggest what is wrong with my cpptraj commands? Also, I'm a
> bit confused if there are close contacts as seen in leap, they should have
> appeared in the cpptraj analysis below, isn't it? thanks
>
> # 06/27/19 09:11:12
> parm RUP-1W0E-gas.prmtop
> trajin RUP-1W0E-gas-min2.rst7
> checkstructure :1-474 reportfile min-structure.txt
> run
> quit
>
>
> > check 1w0e
> Checking '1w0e'....
>
> Warning: The unperturbed charge of the unit (2.000998) is not zero.
>
> Warning: Close contact of 0.966769 angstroms between .R<ARG 81>.A<HH21 21>
> and .R<GL4 349>.A<HE21 14>
>
> Warning: Close contact of 0.878832 angstroms between .R<ARG 81>.A<HE 15>
> and .R<GL4 349>.A<HE11 18>
>
> Warning: Close contact of 1.315493 angstroms between .R<TYR 154>.A<HH 15>
> and .R<VAL 158>.A<HG22 13>
>
> Warning: Close contact of 1.213993 angstroms between .R<ILE 159>.A<HG23 10>
> and .R<SER 163>.A<HG 9>
>
> Warning: Close contact of 1.462009 angstroms between .R<LEU 326>.A<HD11 11>
> and .R<LYS 428>.A<HZ3 20>
>
> Warning: Close contact of 1.452640 angstroms between .R<PHE 410>.A<H 2> and
> .R<GLY 411>.A<H 2>
> Checking parameters for unit '1w0e'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Warnings: 7
> Unit is OK.
>
>
> [xxxxx.hlogin2 rup-3a4-implicit]$ grep ATOM rup-min.pdb | tail -60
> ATOM 7747 HAD1 HEM 473 54.568 82.797 7.244 1.00 0.00
> H
> ATOM 7748 HAD2 HEM 473 54.361 82.119 5.642 1.00 0.00
> H
> ATOM 7749 CBA HEM 473 52.855 83.422 12.138 1.00 0.00
> C
> ATOM 7750 HBA1 HEM 473 52.442 82.904 13.012 1.00 0.00
> H
> ATOM 7751 HBA2 HEM 473 52.376 83.019 11.238 1.00 0.00
> H
> ATOM 7752 CBD HEM 473 52.519 82.198 6.781 1.00 0.00
> C
> ATOM 7753 HBD1 HEM 473 52.211 82.152 7.832 1.00 0.00
> H
> ATOM 7754 HBD2 HEM 473 52.019 81.384 6.242 1.00 0.00
> H
> ATOM 7755 CGD HEM 473 52.024 83.533 6.206 1.00 0.00
> C
> ATOM 7756 CGA HEM 473 52.496 84.915 12.239 1.00 0.00
> C
> ATOM 7757 O1A HEM 473 51.463 85.219 12.804 1.00 0.00
> O
> ATOM 7758 O1D HEM 473 51.045 83.503 5.480 1.00 0.00
> O
> ATOM 7759 O2A HEM 473 53.272 85.742 11.784 1.00 0.00
> O
> ATOM 7760 O2D HEM 473 52.634 84.550 6.500 1.00 0.00
> O
> ATOM 7761 N RUP 474 60.071 86.363 11.368 1.00 0.00
> N
> ATOM 7762 N1 RUP 474 59.865 83.473 8.943 1.00 0.00
> N
> ATOM 7763 C RUP 474 60.527 85.234 10.715 1.00 0.00
> C
> ATOM 7764 C1 RUP 474 60.894 87.354 11.968 1.00 0.00
> C
> ATOM 7765 C2 RUP 474 60.883 87.507 13.374 1.00 0.00
> C
> ATOM 7766 C3 RUP 474 59.964 86.660 14.250 1.00 0.00
> C
> ATOM 7767 C4 RUP 474 61.749 88.437 13.979 1.00 0.00
> C
> ATOM 7768 C5 RUP 474 62.625 89.202 13.196 1.00 0.00
> C
> ATOM 7769 C6 RUP 474 62.622 89.063 11.801 1.00 0.00
> C
> ATOM 7770 C7 RUP 474 61.747 88.159 11.175 1.00 0.00
> C
> ATOM 7771 C8 RUP 474 61.752 88.076 9.649 1.00 0.00
> C
> ATOM 7772 C9 RUP 474 59.421 84.303 10.125 1.00 0.00
> C
> ATOM 7773 C10 RUP 474 58.868 83.412 11.266 1.00 0.00
> C
> ATOM 7774 C11 RUP 474 57.769 82.456 10.774 1.00 0.00
> C
> ATOM 7775 C12 RUP 474 58.255 81.635 9.569 1.00 0.00
> C
> ATOM 7776 C13 RUP 474 58.797 82.549 8.459 1.00 0.00
> C
> ATOM 7777 C14 RUP 474 60.336 84.346 7.825 1.00 0.00
> C
> ATOM 7778 C15 RUP 474 61.260 83.618 6.822 1.00 0.00
> C
> ATOM 7779 C16 RUP 474 62.724 83.549 7.309 1.00 0.00
> C
> ATOM 7780 O RUP 474 61.719 84.979 10.621 1.00 0.00
> O
> ATOM 7781 H RUP 474 59.071 86.480 11.462 1.00 0.00
> H
> ATOM 7782 H1 RUP 474 60.099 85.590 14.048 1.00 0.00
> H
> ATOM 7783 H2 RUP 474 58.911 86.908 14.071 1.00 0.00
> H
> ATOM 7784 H3 RUP 474 60.166 86.817 15.316 1.00 0.00
> H
> ATOM 7785 H4 RUP 474 61.754 88.558 15.059 1.00 0.00
> H
> ATOM 7786 H5 RUP 474 63.307 89.903 13.672 1.00 0.00
> H
> ATOM 7787 H6 RUP 474 63.307 89.655 11.201 1.00 0.00
> H
> ATOM 7788 H7 RUP 474 60.778 87.772 9.248 1.00 0.00
> H
> ATOM 7789 H8 RUP 474 62.504 87.360 9.296 1.00 0.00
> H
> ATOM 7790 H9 RUP 474 61.984 89.052 9.205 1.00 0.00
> H
> ATOM 7791 H10 RUP 474 58.605 84.958 9.794 1.00 0.00
> H
> ATOM 7792 H11 RUP 474 58.465 84.039 12.072 1.00 0.00
> H
> ATOM 7793 H12 RUP 474 59.687 82.826 11.703 1.00 0.00
> H
> ATOM 7794 H13 RUP 474 56.889 83.039 10.479 1.00 0.00
> H
> ATOM 7795 H14 RUP 474 57.468 81.784 11.588 1.00 0.00
> H
> ATOM 7796 H15 RUP 474 57.430 81.033 9.172 1.00 0.00
> H
> ATOM 7797 H16 RUP 474 59.027 80.928 9.888 1.00 0.00
> H
> ATOM 7798 H17 RUP 474 59.174 81.913 7.651 1.00 0.00
> H
> ATOM 7799 H18 RUP 474 57.960 83.136 8.060 1.00 0.00
> H
> ATOM 7800 H19 RUP 474 60.882 85.217 8.203 1.00 0.00
> H
> ATOM 7801 H20 RUP 474 59.467 84.741 7.285 1.00 0.00
> H
> ATOM 7802 H21 RUP 474 61.241 84.165 5.872 1.00 0.00
> H
> ATOM 7803 H22 RUP 474 60.895 82.608 6.607 1.00 0.00
> H
> ATOM 7804 H23 RUP 474 63.122 84.554 7.491 1.00 0.00
> H
> ATOM 7805 H24 RUP 474 63.356 83.062 6.556 1.00 0.00
> H
> ATOM 7806 H25 RUP 474 62.804 82.979 8.240 1.00 0.00
> H
> [r11831vd.hlogin2 [csf3] rup-3a4-implicit]$
>
> On Thu, Jun 27, 2019 at 3:11 AM David Case <david.case.rutgers.edu> wrote:
>
> > On Wed, Jun 26, 2019, Vaibhav Dixit wrote:
> >
> > >The min.rst7 still has close contacts (when I created a pdb and loaded
> > back
> > >in leap).
> > >Is there a faster way to check structures after min, heat jobs to ensure
> > if
> > >they are ok for the next steps in MD simulations?
> >
> > The "checkstructure" command in cpptraj is pretty fast, and can take an
> > rst7
> > file (no need to convert to PDB).
> >
> > If minimization doesn't remove close contacts, there may be something
> > wrong,
> > such as bonds going through rings. Take a visual look at regions that
> > still
> > have bad contacts to see if there is something that is preventing the
> > contacts
> > from being relieved.
> >
> > ....dac
> >
> >
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> >
>
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
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> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
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> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
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>
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Received on Thu Jun 27 2019 - 08:30:07 PDT
