[gmx-users] missing residues in pdb file

[Justin Lemkul]

On Sat, Dec 14, 2013 at 7:03 AM, delara aghaie <d_aghaie at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


==========================================