Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well as [molecule] entry. I have followed the following procedure to #include while creating my first molecule: Run pdb2gmx command. Added #include "ligand.itp" after #include "charmm27.ff/forcefield.itp" but before [ moleculetype ] ; Name nrexcl Protein_chain_A 3 and added at the end: [ molecules ] ; Compound #mols Protein_chain_A 1 LIG 1 SOL 17063
then I have merged protein and ligand coordinates by inserting ATOM lines from ligand.pdb to *.pdb generated after pdb2gmx command. Then. I run editconf, genbox and finally grompp command. After which I got following error: Fatal error: No such moleculetype LIG My both *.itp and *.pdb files contains LIG. How to rectify the error? Thanks in advance. On Tue, Mar 11, 2014 at 1:39 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > Probably you will see that your ligand.itp has an [atomtypes] entry as well > as a [molecule] entry, and the former cannot follow any instance of the > latter. Such an .itp file must be #included to create the first molecule. > You have your protein [molecule] above the #include "ligand.itp" at the > moment, which would cause this problem. > > Mark > > > On Mon, Mar 10, 2014 at 7:09 PM, Nidhi Katyal <nidhikatyal1...@gmail.com > >wrote: > > > To test swiss param parameters, I have generated *.pdb and *.itp files > from > > it. In the genbox command, I have used -ci *.pdb -nmol 2. > > I have included *.itp in the topology as: > > > > ; Include Position restraint file > > ;#ifdef POSRES > > ;#include "posre.itp" > > ;#endif > > > > ;Include ligand topology > > #include "ligand.itp" > > > > ; Include water topology > > #include "charmm27.ff/tip3p.itp" > > > > #ifdef POSRES_WATER > > ; Position restraint for each water oxygen > > [ position_restraints ] > > ; i funct fcx fcy fcz > > 1 1 1000 1000 1000 > > #endif > > > > ; Include topology for ions > > #include "charmm27.ff/ions.itp" > > > > [ system ] > > ; Name > > Protein in water > > > > [ molecules ] > > ; Compound #mols > > Protein_chain_A 1 > > LIG 2 > > SOL 12904 > > > > But after I run grompp command, I get following error: > > > > Fatal error: > > Syntax error - File ligand.itp, line 7 > > Last line read: > > '[ atomtypes ] ' > > Invalid order for directive atomtypes > > > > Please help me rectify the problem of the order getting violated although > > same worked for topology generated by PRODRG. > > > > Thanks in advance. > > > > > > > > On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 3/10/14, 8:21 AM, Nidhi Katyal wrote: > > > > > >> Thanks Justin. I would also like to know the reliability of parameters > > >> generated using swiss param. > > >> > > >> > > >> > > > I have no personal experience with it. My rule is to never trust > > anything > > > from a black-box server without verifying it and assessing any > > information > > > about penalties, deviations, etc. that it provides. > > > > > > -Justin > > > > > > > > > On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul <jalem...@vt.edu> > wrote: > > >> > > >> > > >>> > > >>> On 3/10/14, 2:45 AM, Nidhi Katyal wrote: > > >>> > > >>> Thank you Mark and Justin. > > >>>> Now, I have carried out simulations using PME electrostatics and > using > > >>>> all other > > >>>> parameters (except gromos 96 43a1 ff used) as suggested in > > >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > >>>> gmx-tutorials/lysozyme/ > > >>>> > > >>>> The protein is not loosing its structure now. But the problem is if > I > > >>>> carry out > > >>>> simulations in the presence of experimentally known stabiliser > > generated > > >>>> using > > >>>> ProDrg (keeping all the parameters same while simulating both in the > > >>>> presence > > >>>> and absence of stabiliser), the partial loss of secondary structure > is > > >>>> observed > > >>>> in the presence of stabilizer relative to the case in its absence at > > >>>> 350K > > >>>> thereby implying simulations going against experimental observations > > >>>> (although > > >>>> slight stabilization was observed at 300K). Simulations were > repeated > > >>>> twice with > > >>>> two different force fields. > > >>>> However if I use above em,pr,full parameters with cut-off > > >>>> electrostatics, > > >>>> although secondary structure is lost in the initial stages but I > could > > >>>> clearly > > >>>> see the stabilization behaviour of additive in terms of secondary > > >>>> structure > > >>>> retainment till longer time. Is this observation a matter of chance- > > >>>> reliable or > > >>>> not? What could be the possible reason for not observing such > > >>>> stabilization with > > >>>> better parameters? > > >>>> > > >>>> > > >>>> Cutoff electrostatics are horribly inaccurate. The fact that you > > >>> conveniently see what you hope to when using a plain cutoff is likely > > by > > >>> chance. > > >>> > > >>> The bigger issue is the use of PRODRG parameters. As I have said > > >>> numerous > > >>> times on this list, the parameters it produces are demonstrably > > >>> inaccurate > > >>> and require reparametrization. > > >>> > > >>> http://pubs.acs.org/doi/abs/10.1021/ci100335w > > >>> > > >>> > > >>> -Justin > > >>> > > >>> -- > > >>> ================================================== > > >>> > > >>> Justin A. Lemkul, Ph.D. > > >>> Ruth L. Kirschstein NRSA 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 > > >>> > > >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > >>> http://mackerell.umaryland.edu/~jalemkul > > >>> > > >>> ================================================== > > >>> -- > > >>> Gromacs Users mailing list > > >>> > > >>> * Please search the archive at http://www.gromacs.org/ > > >>> Support/Mailing_Lists/GMX-Users_List before posting! > > >>> > > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >>> > > >>> * For (un)subscribe requests visit > > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor > > >>> send a mail to gmx-users-requ...@gromacs.org. > > >>> > > >>> > > > -- > > > ================================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Ruth L. Kirschstein NRSA 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 > > > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > http://mackerell.umaryland.edu/~jalemkul > > > > > > ================================================== > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at http://www.gromacs.org/ > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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