[gmx-users] missing residues in pdb file

[delara aghaie]

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???
2) in the pdb file I see this pART :
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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
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I want to know if I should add the missing residues before submitting the file to pdb2gmx command?
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?
if so then what about that missing residues which I have not done anything about them???/

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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

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