Dear All,
Changing the cut from 0.8 to 1.0 in cpptraj gives the following. Many of
these lines are strange as they complain about close contacts between atoms
of adjacent residues. Other warnings are about contacts within same
residues, are these artifacts of the cut option > 0.8 or there is a problem
with these residues also? This structure was build using modeler tool
(modweb) to model missing residues from the pdb 1w0e.
Can you please suggest a possible solution to properly minimize the
structure?
Do we expect all contacts to be > 1.5 for a good starting structure?
thank you very much.
[xxxxx.hlogin1 rup-3a4-implicit]$ more min-structure.txt
1 Warning: Atoms 20:THR_2.OG1 and 21:THR_2.HG1 are close (0.97)
1 Warning: Atoms 48:SER_4.OG and 49:SER_4.HG are close (0.97)
1 Warning: Atoms 249:THR_17.OG1 and 250:THR_17.HG1 are close (0.97)
1 Warning: Atoms 405:SER_27.OG and 406:SER_27.HG are close (0.97)
1 Warning: Atoms 422:TYR_28.OH and 423:TYR_28.HH are close (0.99)
1 Warning: Atoms 673:TYR_43.OH and 674:TYR_43.HH are close (0.96)
1 Warning: Atoms 790:TYR_50.OH and 791:TYR_50.HH are close (0.97)
1 Warning: Atoms 939:THR_60.OG1 and 940:THR_60.HG1 are close (0.97)
1 Warning: Atoms 1049:THR_67.OG1 and 1050:THR_67.HG1 are close (0.98)
1 Warning: Atoms 1165:TYR_74.OH and 1166:TYR_74.HH are close (0.97)
1 Warning: Atoms 1180:SER_75.OG and 1181:SER_75.HG are close (0.99)
1 Warning: Atoms 1230:THR_78.OG1 and 1231:THR_78.HG1 are close (0.96)
1 Warning: Atoms 1286:ARG_81.HE and 5646:GL4_349.HE11 are close
(0.88)
1 Warning: Atoms 1292:ARG_81.HH21 and 5642:GL4_349.HE21 are close
(0.97)
1 Warning: Atoms 1440:SER_91.OG and 1441:SER_91.HG are close (0.97)
1 Warning: Atoms 1480:SER_94.OG and 1481:SER_94.HG are close (0.96)
1 Warning: Atoms 1690:SER_106.OG and 1691:SER_106.HG are close (0.97)
1 Warning: Atoms 1739:SER_109.OG and 1740:SER_109.HG are close (0.97)
1 Warning: Atoms 1767:THR_111.OG1 and 1768:THR_111.HG1 are close
(0.96)
1 Warning: Atoms 1801:THR_113.OG1 and 1802:THR_113.HG1 are close
(0.97)
1 Warning: Atoms 1812:SER_114.OG and 1813:SER_114.HG are close (0.97)
1 Warning: Atoms 2026:TYR_127.OH and 2027:TYR_127.HH are close (0.96)
1 Warning: Atoms 2259:THR_141.OG1 and 2260:THR_141.HG1 are close
(0.97)
1 Warning: Atoms 2332:THR_146.OG1 and 2333:THR_146.HG1 are close
(0.97)
1 Warning: Atoms 2455:TYR_154.OH and 2456:TYR_154.HH are close (0.98)
1 Warning: Atoms 2470:SER_155.OG and 2471:SER_155.HG are close (0.98)
1 Warning: Atoms 2548:THR_160.OG1 and 2549:THR_160.HG1 are close
(0.96)
1 Warning: Atoms 2559:SER_161.OG and 2560:SER_161.HG are close (0.98)
1 Warning: Atoms 2573:THR_162.OG1 and 2574:THR_162.HG1 are close
(0.96)
1 Warning: Atoms 2683:SER_170.OG and 2684:SER_170.HG are close (0.99)
1 Warning: Atoms 2866:THR_182.OG1 and 2867:THR_182.HG1 are close
(0.96)
1 Warning: Atoms 3139:SER_197.OG and 3140:SER_197.HG are close (0.97)
1 Warning: Atoms 3172:THR_199.OG1 and 3173:THR_199.HG1 are close
(0.96)
1 Warning: Atoms 3545:THR_221.OG1 and 3546:THR_221.HG1 are close
(0.96)
1 Warning: Atoms 3655:SER_227.OG and 3656:SER_227.HG are close (0.98)
1 Warning: Atoms 3782:SER_234.OG and 3783:SER_234.HG are close (0.97)
1 Warning: Atoms 3866:THR_239.OG1 and 3867:THR_239.HG1 are close
(0.97)
1 Warning: Atoms 4108:SER_253.OG and 4109:SER_253.HG are close (0.97)
1 Warning: Atoms 4150:SER_256.OG and 4151:SER_256.HG are close (0.97)
1 Warning: Atoms 4201:THR_259.OG1 and 4202:THR_259.HG1 are close
(0.97)
1 Warning: Atoms 4227:SER_261.OG and 4228:SER_261.HG are close (0.98)
1 Warning: Atoms 4306:SER_266.OG and 4307:SER_266.HG are close (0.97)
1 Warning: Atoms 4425:SER_274.OG and 4426:SER_274.HG are close (0.97)
1 Warning: Atoms 4556:TYR_282.OH and 4557:TYR_282.HH are close (0.96)
1 Warning: Atoms 4589:THR_284.OG1 and 4590:THR_284.HG1 are close
(0.98)
1 Warning: Atoms 4603:THR_285.OG1 and 4604:THR_285.HG1 are close
(0.97)
1 Warning: Atoms 4614:SER_286.OG and 4615:SER_286.HG are close (0.96)
1 Warning: Atoms 4625:SER_287.OG and 4626:SER_287.HG are close (0.96)
1 Warning: Atoms 4671:SER_290.OG and 4672:SER_290.HG are close (0.97)
1 Warning: Atoms 4744:TYR_294.OH and 4745:TYR_294.HH are close (0.97)
1 Warning: Atoms 4806:THR_298.OG1 and 4807:THR_298.HG1 are close
(0.96)
1 Warning: Atoms 5165:THR_321.OG1 and 5166:THR_321.HG1 are close
(0.97)
1 Warning: Atoms 5182:TYR_322.OH and 5183:TYR_322.HH are close (0.96)
1 Warning: Atoms 5212:THR_324.OG1 and 5213:THR_324.HG1 are close
(0.97)
1 Warning: Atoms 5313:TYR_330.OH and 5314:TYR_330.HH are close (0.96)
1 Warning: Atoms 5440:THR_338.OG1 and 5441:THR_338.HG1 are close
(0.96)
1 Warning: Atoms 5640:GL4_349.OE1 and 5646:GL4_349.HE11 are close
(0.96)
1 Warning: Atoms 5640:GL4_349.OE1 and 5647:GL4_349.HE12 are close
(0.96)
1 Warning: Atoms 5641:GL4_349.OE2 and 5642:GL4_349.HE21 are close
(0.96)
1 Warning: Atoms 5641:GL4_349.OE2 and 5645:GL4_349.HE22 are close
(0.96)
1 Warning: Atoms 6030:SER_373.OG and 6031:SER_373.HG are close (0.97)
1 Warning: Atoms 6047:TYR_374.OH and 6048:TYR_374.HH are close (0.96)
1 Warning: Atoms 6186:TYR_382.OH and 6187:TYR_382.HH are close (0.96)
1 Warning: Atoms 6228:THR_384.OG1 and 6229:THR_384.HG1 are close
(0.97)
1 Warning: Atoms 6417:SER_395.OG and 6418:SER_395.HG are close (0.98)
1 Warning: Atoms 6585:TYR_405.OH and 6586:TYR_405.HH are close (0.96)
1 Warning: Atoms 6625:TYR_407.OH and 6626:TYR_407.HH are close (0.97)
1 Warning: Atoms 6643:THR_408.OG1 and 6644:THR_408.HG1 are close
(0.97)
1 Warning: Atoms 6695:SER_412.OG and 6696:SER_412.HG are close (0.96)
1 Warning: Atoms 6752:AS4_416.OD1 and 6758:AS4_416.HD11 are close
(0.96)
1 Warning: Atoms 6752:AS4_416.OD1 and 6759:AS4_416.HD12 are close
(0.96)
1 Warning: Atoms 6753:AS4_416.OD2 and 6754:AS4_416.HD21 are close
(0.96)
1 Warning: Atoms 6753:AS4_416.OD2 and 6757:AS4_416.HD22 are close
(0.96)
1 Warning: Atoms 6832:ARG_421.NH2 and 6833:ARG_421.HH21 are close
(1.00)
1 Warning: Atoms 6832:ARG_421.NH2 and 6834:ARG_421.HH22 are close
(1.00)
1 Warning: Atoms 7140:SER_439.OG and 7141:SER_439.HG are close (0.97)
1 Warning: Atoms 7258:THR_446.OG1 and 7259:THR_446.HG1 are close
(0.97)
1 Warning: Atoms 7379:SER_453.OG and 7380:SER_453.HG are close (0.97)
1 Warning: Atoms 7647:SER_470.OG and 7648:SER_470.HG are close (0.99)
On Thu, Jun 27, 2019 at 4:15 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> >
> > 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,
> > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> > 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
> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >
> > ORCID ID: https://orcid.org/0000-0003-4015-2941
> >
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >
> > P Please consider the environment before printing this e-mail
> > _______________________________________________
> > AMBER mailing list
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
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
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
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Received on Thu Jun 27 2019 - 09:00:03 PDT
