[gmx-users] Re: Bonds break while Minimising using solved
plmallip at mail.uh.edu
plmallip at mail.uh.edu
Thu Sep 4 20:02:28 CEST 2008
First of all I would like to thank Justin, for giving me a clue about
checking the bonds in "chain_C.itp" file. When I removed all those
unexpected bonds, minimization as successful.
To summarize,
I want to minimize a pentamer by imposing distance restraints in one of
the chains. This chain has 14 residues missing and the distance between
the end residues (residue 162 and 163 here) is 12 A (1.2 nm). These are
the steps I followed to run minimization using distance restraints
1. pdb2gmx -ff G43a1 -f chnr.pdb -o chnr1.gro -p chnr1.top -ter -his -ss -asp -glu -water spce
I didn't use -missing option, as I didn't observe any difference either way
2. Included the following distance restraints in the chain_C.itp file
#ifdef DISRES
[ distance_restraints ]
;ai aj type index type' low up1 up2 fac
1703 1712 1 0 1 1.15 1.20 1.25 1.0
#endif
3.
Removed unexpected bonds between the two residues. This is the step
which I skipped and has been giving me an error "Warning: 1-4
interaction between
6151 and 6160 is at distance 1.387 which is larger than the 1-4 table size". I end up in a structure with missing bonds.
Here is part of the chain_c.itp file with changes
; File 'chnrc_C.itp' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Thu Sep 4 10:58:17 2008
;
; This is your include topology file
; "I Feel a Great Disturbance in the Force" (The Emperor Strikes Back)
;
[ moleculetype ]
; Name nrexcl
Protein_C 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1701 N 162 LEU N 733 -0.28 14.0067 ; qtot -7.28
1702 H 162 LEU H 733 0.28 1.008 ; qtot -7
1703 CH1 162 LEU CA 734 0 13.019 ; qtot -7
1704 CH2 162 LEU CB 734 0 14.027 ; qtot -7
1705 CH1 162 LEU CG 735 0 13.019 ; qtot -7
1706 CH3 162 LEU CD1 735 0 15.035 ; qtot -7
1707 CH3 162 LEU CD2 735 0 15.035 ; qtot -7
1708 C 162 LEU C 736 0.38 12.011 ; qtot -6.62
1709 O 162 LEU O 736 -0.38 15.9994 ; qtot -7
1710 N 163 ILE N 737 -0.28 14.0067 ; qtot -7.28
1711 H 163 ILE H 737 0.28 1.008 ; qtot -7
1712 CH1 163 ILE CA 738 0 13.019 ; qtot -7
1713 CH1 163 ILE CB 739 0 13.019 ; qtot -7
1714 CH2 163 ILE CG1 739 0 14.027 ; qtot -7
1715 CH3 163 ILE CG2 739 0 15.035 ; qtot -7
1716 CH3 163 ILE CD 739 0 15.035 ; qtot -7
1717 C 163 ILE C 740 0.38 12.011 ; qtot -6.62
1718 O 163 ILE O 740 -0.38 15.9994 ; qtot -7
[ bonds ]
; ai aj funct c0 c1 c2 c3
1699 1701 2 gb_9
1701 1702 2 gb_2
1701 1703 2 gb_20
1703 1704 2 gb_26
1703 1708 2 gb_26
1704 1705 2 gb_26
1705 1706 2 gb_26
1705 1707 2 gb_26
1708 1709 2 gb_4
;1708 1710 2 gb_9
1710 1711 2 gb_2
1710 1712 2 gb_20
1712 1713 2 gb_26
1712 1717 2 gb_26
1713 1714 2 gb_26
1713 1715 2 gb_26
1714 1716 2 gb_26
1717 1718 2 gb_4
1717 1719 2 gb_9
[ pairs ]
; ai aj funct c0 c1 c2 c3
1701 1705 1
1701 1709 1
;1701 1710 1
1702 1704 1
1702 1708 1
1703 1706 1
1703 1707 1
;1703 1711 1
;1703 1712 1
1704 1709 1
;1704 1710 1
1705 1708 1
;1708 1713 1
;1708 1717 1
;1709 1711 1
;1709 1712 1
1710 1714 1
1710 1715 1
1710 1718 1
1710 1719 1
1711 1713 1
1711 1717 1
1712 1716 1
1712 1720 1
1712 1721 1
1713 1718 1
1713 1719 1
1714 1717 1
1715 1716 1
1715 1717 1
1717 1722 1
1717 1726 1
1718 1720 1
1718 1721 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
1701 1703 1704 2 ga_12
1701 1703 1708 2 ga_12
1704 1703 1708 2 ga_12
1703 1704 1705 2 ga_14
1704 1705 1706 2 ga_14
1704 1705 1707 2 ga_14
1706 1705 1707 2 ga_14
1703 1708 1709 2 ga_29
;1703 1708 1710 2 ga_18
;1709 1708 1710 2 ga_32
;1708 1710 1711 2 ga_31
;1708 1710 1712 2 ga_30
1711 1710 1712 2 ga_17
1710 1712 1713 2 ga_12
1710 1712 1717 2 ga_12
1713 1712 1717 2 ga_12
1712 1713 1714 2 ga_14
1712 1713 1715 2 ga_14
1714 1713 1715 2 ga_14
1713 1714 1716 2 ga_14
1712 1717 1718 2 ga_29
1712 1717 1719 2 ga_18
1718 1717 1719 2 ga_32
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1694 1699 1701 1703 1 gd_4
1699 1701 1703 1708 1 gd_19
1701 1703 1704 1705 1 gd_17
;1701 1703 1708 1710 1 gd_20
1703 1704 1705 1706 1 gd_17
;1703 1708 1710 1712 1 gd_4
;1708 1710 1712 1717 1 gd_19
1710 1712 1713 1714 1 gd_17
1710 1712 1717 1719 1 gd_20
1712 1713 1714 1716 1 gd_17
1712 1717 1719 1721 1 gd_4
1717 1719 1721 1726 1 gd_19
1719 1721 1722 1723 1 gd_17
1719 1721 1726 1728 1 gd_20
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
1701 1699 1703 1702 2 gi_1
1703 1701 1708 1704 2 gi_2
1704 1706 1707 1705 2 gi_2
;1708 1703 1710 1709 2 gi_1
;1710 1708 1712 1711 2 gi_1
1712 1710 1717 1713 2 gi_2
1712 1715 1714 1713 2 gi_2
1717 1712 1719 1718 2 gi_1
1719 1717 1721 1720 2 gi_1
#ifdef DISRES
[ distance_restraints ]
;ai aj type index type' low up1 up2 fac
1703 1712 1 0 1 1.15 1.20 1.25 1.0
#endif
4. Included "define = -DDISRES" in the .mdp file for minimisation
Once again, I appreciate Justin for giving me helpful hints in sorting out where I was going wrong.
Thanks & regards,
Latha.
>
So you have an incomplete protein backbone, with some odd numbering.
What command did you give pdb2gmx to generate this topology? Did you
use the -missing flag? If so, the topology may be badly broken and
unexpected bonds defined. Look closely at your [ bonds ] section in
"chain_C.itp" in case you have some bonds that you are not expecting!
I
checked the .itp file and I found some unexpected bonding between the
two residues. When, I removed all those bonds, it worked.
> Date: Wed, 03 Sep 2008 20:33:58 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Bonds break while Minimising using
> distance restraints
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <48BF2CF6.6070207 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> plmallip at mail.uh.edu wrote:
>
> > My protein has 5 chains. 1703 & 1712 are the numbers from
> chainC.itp
> > file. This includes the distance restraints -
> >
> > #ifdef DDISRES
> > [ distance_restraints ]
> > ;ai aj type index type' low up1
> up2 fac
> > 1703 1712 1 0
> 1 1.15 1.20 1.25 1.0
> > #endif
> >
> > 6151 & 6160 atoms are the numbers from .gro file reported by
> the .job
> > file. 6151 is N of residue 584 and 1703 is CA of the same
> redsidue.
> > Residue 584 & 585 are placed have 14 residues missing between
> them. 6160
> > is N of residue 585 & 1712 is the corresponding CA.
>
> So you have an incomplete protein backbone, with some odd
> numbering. What
> command did you give pdb2gmx to generate this topology?
> Did you use the
> -missing flag? If so, the topology may be badly broken and
> unexpected bonds
> defined. Look closely at your [ bonds ] section in
> "chain_C.itp" in case you
> have some bonds that you are not expecting!
>
> Do you have complete residues for each of those that contain
> atoms 6151, 6160,
> 1703 and 1712? The non-sequential numbering (with 4000-
> atom separation!) does
> not indicate that these atoms should be in the same residues.
>
> Is your structure one that is available in the PDB?
> Perhaps it would be much
> easier to diagnose this if I could see the structure. I'd
> be willing to have a
> look at your structure file, if you'd like to send it to me
> privately. I'm
> somewhat intrigued as to what the problem is :)
>
> I would be willing to bet that there is something within that
> chain topology
> that is causing mdrun to find a 1-4 interaction between atoms
> 6151 and 6160.
>
> -Justin
>
> >
> >
> > Thanks & regards,
> > Latha.
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