[gmx-users] H-atoms in .hdb file

[Shima Arasteh]

I added this line to the residuetypes.dat file:
FOR   Protein

Then running this command:
pdb2gmx -f protein.pdb -water spc -ter

Written as blow:

Processing chain 1 (177 atoms, 25 residues)
Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
Identified residue VAL1 as a starting terminus.
Identified residue GLY24 as a ending terminus.

Asked for terminus:
I chose "none" as the N-terminus.
 
Getting this:
 Processing chain 1 (177 atoms, 25 residues)
Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
Identified residue VAL1 as a starting terminus.
Identified residue GLY24 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for VAL-1
 0: NH3+
 1: NH2
 2: None
2
Start terminus VAL-1: None
Select end terminus type for GLY-24
 0: COO-
 1: COOH
 2: None
0
End terminus GLY-24: COO-

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1035

Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.


Would you helping me with it with your useful suggestions?




Sincerely,
Shima


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Wednesday, June 27, 2012 2:58 PM
Subject: Re: [gmx-users] H-atoms in .hdb file



On 6/27/12 3:38 AM, Shima Arasteh wrote:
>
>
> As Justin suggested me, I added the FOR residue to the .rtp file of FF and then added the FOR as a protein in residuetypes.dat . FOR is the first residue in protein chain. I chose none as the N-terminus . But after processing the .pdb file the FOR is identified itself but "not" identified as protein.
>

How so?  What line did you add to residuetypes.dat, and what was the exact 
problematic output of pdb2gmx?

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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