Dear All (and David)
I got the syntax right, but the rst7 file is still failing to load in vmd.
parmed checkvalidity gave same two warnings.
Please suggest, if using these final prmtop/rst7 files for MD is
meaningful? thanks
vmd gives the messages shown below, but fails to display and load the frame.
> deletebond :421 :420
Deleting the 1 bonds found between :421 and :420
> outparm com5.prmtop com5.rst7
Outputting Amber topology file com5.prmtop and restart com5.rst7
ParmEd: a Parameter file Editor
Loaded Amber topology file com5.prmtop with coordinates from com5.rst7
Reading input from STDIN...
*> checkvalidity*
Determining validity of prmtop
2 total warnings
MissingDisulfide: Detected two cysteine residues whose sulfur atoms are
within 3
Angstroms. Rename CYS to CYX in the PDB file and use the
'bond' command in tleap to create the disulfide bond
LongBondWarning: Atoms 7253 (GLN 449 [C]) and 7255 (ALA 450 [N]) are bonded
(equilibrium length 1.335 A) but are 4.826 A apart. This
often
indicates gaps in the original sequence and should be
checked
carefully.
*> printbonds :420,421*
Atom 1 Atom 2 R eq Frc Cnst Distance
Energy
6761 N ( N) 7790 C3 ( c) 1.3790 427.6000 1.3105
2.0071
6762 CD ( CT) 6761 N ( N) 1.4490 337.0000 1.4814
0.3547
6765 CG ( CT) 6762 CD ( CT) 1.5380 300.9000 1.4985
0.4686
6768 CB ( CT) 6765 CG ( CT) 1.5380 300.9000 1.4941
0.5792
6771 CA ( CX) 6761 N ( N) 1.4490 337.0000 1.4745
0.2185
6771 CA ( CX) 6768 CB ( CT) 1.5260 310.0000 1.5218
0.0055
6773 C ( C) 6771 CA ( CX) 1.5220 317.0000 1.5324
0.0346
6773 C ( C) 6775 N ( N) 1.3350 490.0000 1.3384
0.0057
6774 O ( O) 6773 C ( C) 1.2290 570.0000 1.2361
0.0290
6744 CA ( CX) 6742 N ( N) 1.4490 337.0000 1.4869
0.4839
6746 CB ( 3C) 6744 CA ( CX) 1.5260 310.0000 1.5402
0.0624
6748 CG2 ( CT) 6746 CB ( 3C) 1.5260 310.0000 1.5186
0.0169
6752 CG1 ( 2C) 6746 CB ( 3C) 1.5260 310.0000 1.5371
0.0382
6755 CD1 ( CT) 6752 CG1 ( 2C) 1.5260 310.0000 1.5089
0.0907
6759 C ( C) 6744 CA ( CX) 1.5220 317.0000 1.5399
0.1016
6759 C ( C) 7783 N1 ( n) 1.3790 427.6000 0.7438
172.5172
6760 O ( O) 6759 C ( C) 1.2290 570.0000 1.2231
0.0198
6740 C ( C) 6742 N ( N) 1.3350 490.0000 1.3349
0.0000
6763 HD2 ( H1) 6762 CD ( CT) 1.0970 330.6000 1.0900
0.0162
6764 HD3 ( H1) 6762 CD ( CT) 1.0970 330.6000 1.0900
0.0162
6766 HG2 ( HC) 6765 CG ( CT) 1.0970 330.6000 1.0900
0.0162
6767 HG3 ( HC) 6765 CG ( CT) 1.0970 330.6000 1.0900
0.0162
6769 HB2 ( HC) 6768 CB ( CT) 1.0970 330.6000 1.0900
0.0162
6770 HB3 ( HC) 6768 CB ( CT) 1.0970 330.6000 1.0900
0.0162
6772 HA ( H1) 6771 CA ( CX) 1.0900 340.0000 1.0900
0.0000
6743 H ( H) 6742 N ( N) 1.0130 403.2000 1.0100
0.0036
6745 HA ( H1) 6744 CA ( CX) 1.0900 340.0000 1.0900
0.0000
6747 HB ( HC) 6746 CB ( 3C) 1.0900 340.0000 1.0900
0.0000
6749 HG21 ( HC) 6748 CG2 ( CT) 1.0970 330.6000 1.0900
0.0162
6750 HG22 ( HC) 6748 CG2 ( CT) 1.0970 330.6000 1.0900
0.0162
6751 HG23 ( HC) 6748 CG2 ( CT) 1.0970 330.6000 1.0900
0.0162
6753 HG12 ( HC) 6752 CG1 ( 2C) 1.0900 340.0000 1.0900
0.0000
6754 HG13 ( HC) 6752 CG1 ( 2C) 1.0900 340.0000 1.0900
0.0000
6756 HD11 ( HC) 6755 CD1 ( CT) 1.0970 330.6000 1.0900
0.0162
6757 HD12 ( HC) 6755 CD1 ( CT) 1.0970 330.6000 1.0900
0.0162
6758 HD13 ( HC) 6755 CD1 ( CT) 1.0970 330.6000 1.0900
0.0162
> quit
Done!
*vmd terminal output*
(base) [exx.c107739 xleap-mol2]$ vmd com5.prmtop com5.rst7
/home/exx/Downloads/vmd-1.9.3/vmd/vmd_LINUXAMD64: /lib64/libGL.so.1: no
version information available (required by
/home/exx/Downloads/vmd-1.9.3/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info)
http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd.ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 12 CPUs detected.
Info) CPU features: SSE2 AVX AVX2 FMA
Info) Free system memory: 58GB (92%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator:
Info) [0] GeForce RTX 2080 SUPER 48 SM_7.5 @ 1.82 GHz, 7.8GB RAM, KTO, AE3,
ZCP
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option. Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: GeForce RTX 2080 SUPER/PCIe/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture
(4)
Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info) Compiling 1 OptiX shaders on 1 target GPU...
Info) Dynamically loaded 2 plugins in directory:
Info) /home/exx/Downloads/vmd-1.9.3/vmd/plugins/LINUXAMD64/molfile
Info) File loading in progress, please wait.
Info) Using plugin parm7 for structure file com5.prmtop
*Info) Analyzing structure ...*
Info) Atoms: 7858
Info) Bonds: 7963
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 482
Info) Waters: 0
*Warning) Unusual bond between residues: 420 (protein) and 482
(none)Warning) Unusual bond between residues: 421 (protein) and 482 (none)*
Info) Segments: 1
Info) Fragments: 1 Protein: 2 Nucleic: 0
rst7plugin) Title:
rst7plugin) This file contains velocity info.
rst7plugin) The Restartcrd has 7858 atoms.
Info) Using plugin rst7 for coordinates from file com5.rst7
rst7plugin) Importing velocities from restart file.
Info) Finished with coordinate file com5.rst7.
On Thu, Feb 20, 2020 at 9:16 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear All (and David),
> I tried the following but still can't get rid of the long-amide bond.
> The residue numbers are correct here and I tried using Amber Mask (sec.
> 19.1 manual) syntax, but that also gives the same error. vmd still can't
> read the rst7 file and pdb (from ampdb shows the long aminde-bond). The
> help deletebond command shows the same message as in the manual (below).
> Please help me understand the correct mask usage here.
>
> > deletebond 420 421 parm com2.prmtop
> Using parm com2.prmtop
> *Bad command deleteBond:*
> deleteBond <mask1> <mask2>
> > outparm com2-1.prmtop com2-1.rst7
> > deletebond *:420,421 *parmt com2.prmtop
> Bad command deleteBond:
> deleteBond <mask1> <mask2>
> >
> > help deletebond
> deleteBond <mask1> <mask2> [parm <idx>|<name>]
>
> This action deletes any bonds that occur between the atoms in two
> masks.
>
> - <mask1> : Amber mask defining one of the atoms in a bond
> - <mask2> : Amber mask defining the other atom in the bond
> - [verbose] : Print out every bond that is deleted as well as the
> number of other valence terms that were eliminated.
>
> All bonds will be matched in which one atom comes from <mask1> and the
> other
> atom comes from <mask2>. This action will also delete any other
> valence term
> (like angles and dihedrals) that would get severed by the deletion of
> one of
> the bonds.
>
> >
>
> On Wed, Feb 19, 2020 at 10:56 PM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Wed, Feb 19, 2020, Vaibhav Dixit wrote:
>>
>> >I removed the TER card between residues 420 and 421, then used bond
>> command
>> >as shown below.
>>
>> >This has bonded the non-std residue CYS-HEM with main chain as expected.
>> >tleap adds amide bond between 420 and 421, which I want to delete using
>> >parmed deletebond command.
>>
>> >> deleteBond :420,421
>> >Bad command deleteBond:
>>
>> The deleteBond command requires two masks; type "help deleteBond" to see
>> more info.
>>
>> ...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
>
>
--
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 Feb 20 2020 - 04:30:02 PST
