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