use -missing in last of command pdb2gmx On Mon, Aug 25, 2014 at 10:54 AM, neha bharti <nehabharty...@gmail.com> wrote: > Hello All > > I am performing Molecular dynamics simulation of protein-ligand complex > using charmm36 force field in popc lipid. > > I downloaded the protein ligand complex pdb file. And as mentioned in > Justin A. Lemkul protein-ligand complex tutorial I have seperate ligand and > protein from pdb file. > > My protein contain some missing residues so I have homology modeled the > protein taking the same pdb file as target and templet. > > At the time of Building the complex step I am using the homology modelled > protein. > > Can I add the ligand in that file as shown in tutorial: > > 163ASN C 1691 0.621 -0.740 -0.126 > 163ASN O1 1692 0.624 -0.616 -0.140 > 163ASN O2 1693 0.683 -0.703 -0.011 > 1JZ4 C4 1 2.429 -2.412 -0.007 > 1JZ4 C14 2 2.392 -2.470 -0.139 > 1JZ4 C13 3 2.246 -2.441 -0.181 > 1JZ4 C12 4 2.229 -2.519 -0.308 > 1JZ4 C11 5 2.169 -2.646 -0.295 > > because due to homology modeling it might be possible that the coordinates > of the protein will get change?? > > Or I should use maxwarn option to avoid the error message of missing > residues of protein pdb file and no need of homology modelling?? > > Please Help > -- > 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
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