1. Did you re-run pdb2gmx after modifying the .rtp file? Yes.. I do run with modified .rtp file but output was same as previous.
2. Have you looked into the [bonds] directive in the .top file that pdb2gmx created to see if anything is out of place? Every line should have 5 entries: [bonds] directive contains only 3 entries for every line. atom_i atom_j funct b0 kb the entries present in [bonds] directive in the .top file was atom_i atom_j funct c0 c1 c2 c3. These are the some warnings for Zinc and calcium ions for pdb2gmx Warning: Residue ZN264 in chain has different type (Ion) from starting residue PHE100 (Protein). Warning: Residue ZN265 in chain has different type (Ion) from starting residue PHE100 (Protein). Warning: Residue CA266 in chain has different type (Ion) from starting residue PHE100 (Protein). Warning: Residue CA267 in chain has different type (Ion) from starting residue PHE100 (Protein). Warning: Residue CA268 in chain has different type (Ion) from starting residue PHE100 (Protein). Thanks Justin .., I appreciate your help for whole week. I stopped here (give up). --Rama _______________________________________________________ Ramakrishna Koppisetti | Research Specialist | Protein NMR group | Biochemistry Department | University of Missouri | Columbia, USA | Email Id : koppiset...@missouri.edu | Mobile No : +573-529-5932 | _______________________________________________________ On Thu, Sep 12, 2013 at 11:27 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/12/13 11:03 AM, Rama Krishna Koppisetti wrote: > >> Hi, >> These are the parameters I kept in the .rtp file for DMPC molecule. Still >> getting same error message should I need to look at somewhere else. >> >> [ bondedtypes ] >> ; Col 1: Type of bond >> ; Col 2: Type of angles >> ; Col 3: Type of proper dihedrals >> ; Col 4: Type of improper dihedrals >> ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. >> ; Col 6: Number of excluded neighbors for nonbonded interactions >> ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 >> ; Col 8: Remove propers over the same bond as an improper if it is 1 >> ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih >> 1 1 3 1 1 3 1 0 >> >> >> [ DMPC ] >> [ atoms ] >> ; name type charge chgnr >> CN1 LC3 0.4000 1 >> CN2 LC3 0.4000 1 >> CN3 LC3 0.4000 1 >> NTM LNL -0.5000 1 >> CA LH2 0.3000 1 >> CB LC2 0.4000 2 >> OA LOS -0.8000 2 >> P LP 1.7000 2 >> OB LOM -0.8000 2 >> OC LOM -0.8000 2 >> OD LOS -0.7000 2 >> [ bonds ] >> ; ai aj >> CN1 NTM >> CN2 NTM >> CN3 NTM >> NTM CA >> CA CB >> CB OA >> OA P >> P OB >> P OC >> P OD >> OD CC >> CC CD >> CD OE >> CD CE >> OE C1A >> > > If you don't specify bond lengths and force constants here, they need to > be present in ffbonded.itp. Either approach is fine. The only issue you > had before was that you included a function type, which would have > explained the error you got before. > > > [ angles ] >> ; ai aj ak funct angle fc >> CN1 NTM CN2 2 109.50 520.00 >> CN1 NTM CN3 2 109.50 520.00 >> CN1 NTM CA 2 109.50 520.00 >> CN2 NTM CN3 2 109.50 520.00 >> CN2 NTM CA 2 109.50 520.00 >> CN3 NTM CA 2 109.50 520.00 >> NTM CA CB 2 111.00 530.00 >> CA CB OA 2 111.00 530.00 >> CB OA P 2 120.00 530.00 >> OA P OC 2 109.60 450.00 >> OA P OB 2 109.60 450.00 >> OA P OD 2 103.00 420.00 >> P OD CC 2 120.00 530.00 >> OC P OB 2 120.00 780.00 >> OC P OD 2 109.60 450.00 >> > > Same as with [bonds], you cannot have a function type specified here. > > > [ dihedrals ] >> ; ai aj ak al funct ph0 cp mult >> CN3 NTM CA CB 1 0.00 3.77 3 >> NTM CA CB OA 1 0.00 8.62 3 >> CA CB OA P 1 0.00 3.77 3 >> CB OA P OD 1 0.00 3.19 3 >> OA P OD CC 1 0.00 3.19 3 >> P OD CC CD 1 0.00 3.77 3 >> OD CC CD CE 1 0.00 5.92 3 >> CC CD OE C1A 1 0.00 3.77 3 >> CC CD CE OG 1 0.00 5.92 3 >> CD OE C1A C1B 1 180.00 24.00 2 >> CD CE OG C2A 1 0.00 3.77 3 >> OE C1A C1B C1C 1 0.00 1.00 6 >> [ impropers ] >> ; GROMOS improper dihedrals >> ; ai aj ak al funct angle fc >> CD OE CE CC 2 35.26 334.72 >> C1A OE OF C1B 2 0.00 167.36 >> C2A OG OH C2B 2 0.00 167.36 >> >> > Same applies for the dihedrals and impropers. > > To avoid another string of incomplete replies, please answer the following > questions directly. Remember, I'm trying (very hard) to help you resolve > this and we're just spinning our wheels. > > 1. Did you re-run pdb2gmx after modifying the .rtp file? > 2. Have you looked into the [bonds] directive in the .top file that > pdb2gmx created to see if anything is out of place? Every line should have > 5 entries: > > atom_i atom_j funct b0 kb > > Anything more or less (in this case) is wrong. Can you identify any > problematic lines, and if so, to which atoms do they apply? > > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? 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