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" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Re: Bonds break while Minimising using > distance restraints > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > [EMAIL PROTECTED] 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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