[gmx-users] How to simulate peptide capped with ACE?

Alan Dodd anoddlad at yahoo.com
Wed Jul 11 20:32:23 CEST 2007

For some reason this didn't send to the mailing list...

I use C-terminal amidated peptides, which sounds similar to what you're trying to achieve.  Still, more info about what you've done would have made this reply rather shorter.  Is the residue still there after pdb2gmx, for instance?  I've never seen grompp remove residues, normally, it exits if something is wrong.

What I do is:
I have a residue in my .rtp for the amino group, and specify the amide as a seperate residue in .  When running pdb2gmx, I select the "none" option for that terminus.  This works well for me, never seen a problem.  Perhaps the format of your ACE entry in your .rtp isn't appropriate... if you're using the preexisting entry, it won't work because there isn't a bond designated to connect it to the backbone (I think).  For instance, I have the line:
    -C     N
in my [ bonds ] section - check the 3.3 manual, section 5.5.1.

----- Original Message ----
From: "fufengliu at tju.edu.cn" <fufengliu at tju.edu.cn>
To: gmx-users at gromacs.org
Sent: Wednesday, July 11, 2007 2:41:17 PM
Subject: [gmx-users] How to simulate peptide capped with ACE?

Hi, Mark
Thank you for your reply. I¡¯m sorry that I didn¡¯t say my question in detail. I
want to simulate the peptide capped with ACE group. I use the ffG43a1 force field.
I read some suggestions in mailing list archive and named the residue in the
initial structure. I used pdb2gmx and it works well. But when I run grompp, I got
the warning ¡± No default G96Angle types, using zeroes.¡±. I check the structure
and found that the ACE group disappears. Can you tell me why or how to correct it?

Thank you very much! 
fufeng Liu  

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