Hi, I think this was answered earlier but I didn't quite understand the answer given.
Hi Hitesh, The posre.itp file only contains a header [ position_restraints ] followed by a list of atom numbers and restraint force constants. Check chapter 5 of the manual for how and what. For a ligand it's probably best to directly add the [ position_restraints ] section in the file with the [ molecule_type ] definition, possibly enclosed by the statements #ifdef POSRES and #endif. Mind that the aom numbers need to refer to the atom numbers within the molecule_type definition and are not related to the atom numbers in the coordinate file. Cheers, Tsjerk On Wed, Apr 15, 2009 at 9:05 AM, Hitesh singla <hiteshsingla123 at gmail.com <http://www.gromacs.org/mailman/listinfo/gmx-users>> wrote: >* Dear all, *>* *>* I have generated .itp file for ligand using PRODRG server which i included *>* in topology file. Now for position restrained dynamics, i wanted to restrain *>* atom positions for ligand and protein . But porse.itp which generated using *>* pdb2gmx contain restraints for protein only. Kindly provide me the solution *>* to restrain ligand atoms. *>* *>* Thanks, *>* Hitesh Singla * I am trying to do what Hitesh tried to do..get a pos restraint on both my protein and ligand....I found that -DPOSRES only takes into account 1 posre.itp file...so I appended the atom numbers of my ligand (2519-2531) to the end of the posre file for my protein (1-2518). Then I tried running grompp on this and it gave me the error ------------------------------------------------------- Program grompp, VERSION 3.3.3 Source code file: ../../../src/kernel/toppush.c, line: 1193 Fatal error: [ file "posre.itp", line 2015 ]: Atom index (2519) in position_restraints out of bounds (1-2518). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. ------------------------------------------------------- Also, fyi, earlier for energy minimization, I had included the ff for the itp file in [forcefield] section and included HSL (my ligand) in the [molecule] section after putting the coords for the HSL into my protein pdb file. See parts of the top file below: ; File 'BR6.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Wed Apr 29 11:35:48 2009 ; ; This is your topology file ; "I'll Match Your DNA" (Red Hot Chili Peppers) ; ; Include forcefield parameters #include "ffgmx.itp" #include "C4AHLdbMarc.itp" [ moleculetype ] ; Name nrexcl Protein_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NL 1 MET N 1 0.129 14.0067 ; qtot 0.129 2 H 1 MET H1 1 0.248 1.008 ; qtot 0.377 3 H 1 MET H2 1 0.248 1.008 ; qtot 0.625 4 H 1 MET H3 1 0.248 1.008 ; qtot 0.873 5 CH1 1 MET CA 1 0.127 13.019 ; qtot 1 6 CH2 1 MET CB 2 0 14.027 ; qtot 1 7 CH2 1 MET CG 3 0 14.027 ; qtot 1 8 S ;etc....end of file below 2509 2507 2514 2510 2 2509 2512 2511 2510 2 2509 2516 2515 2514 2 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_A 1 HSL 1 SOL 1 SOL 12480 Na 11 So, is it not possible in GROMACS to restrain multiple molecules together? If it is, how do you do this? Thanks in advance, Halie Shah U of H Briggs Lab
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