On Sat, Dec 14, 2013 at 7:03 AM, delara aghaie <d_agh...@yahoo.com> wrote:
> Dear Gromacs users, I am going to simulate human serum albumin( HSA) .. > The pdb file contains warfarin as well. > > Now I have two questions: > 1) to delete warfarin which lines should be removed? only those starting > with HETATM or more??? > The .pdb file tells you what the warfarin residue name is. Delete those lines if you don't need them. > 2) in the pdb file I see this pART : > ---------------- > > EMARK 465 > REMARK 465 MISSING RESIDUES > REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE > REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN > REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) > REMARK 465 > REMARK 465 M RES C SSSEQI > REMARK 465 ASP A 1 > REMARK 465 ALA A 2 > REMARK 465 HIS A 3 > REMARK 465 LYS A 4 > REMARK 465 LEU A 583 > REMARK 465 GLY A 584 > ------------------- > I want to know if I should add the missing residues before submitting the > file to pdb2gmx command? > That depends on whether or not they are functionally significant. Based on their numbering, I would guess they are floppy termini and may not be relevant, but it is a choice you must make based on reading about the structure itself and your knowledge of the protein's biology and function. > The other thing is that when I run pdb2gmx, only I get this error: ( does > the error says that there is something wrong with line 491? > Line 491 is the line in the source code that triggers the error; it has nothing to do with your coordinate file. > if so then what about that missing residues which I have not done anything > about them???/ > > As I suspected above, they are terminal residues. pdb2gmx only complains about missing residues when something is missing within the chain. If you otherwise have consecutive numbering and sensible geometry, pdb2gmx is perfectly happy. But, as you will note from the fatal error shown below, pdb2gmx hasn't even been able to open your file to complain about anything else. > -------------- > > Program pdb2gmx_d, VERSION 4.5.5 > Source code file: futil.c, line: 491 > File input/output error: > 2BXD.pdb > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > ------------- > This error means the file doesn't exist in the working directory or doesn't have the correct permissions to be opened. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ========================================== -- 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.