[gmx-users] Add acetyl and amide caps to a peptide with pdb2gmx

[Justin A. Lemkul]

Stephane Abel wrote:
> Hi gromacs users
> 
> I would like to add a acetyl and amide caps (N and C term) to a peptide 
> for subsequent simulations with with GMX(v4.05) and the ffG53a6 ff . For 
> this purpose i have added manually the missing atoms in my pdb files 
> taken from the protein databank
> 
> My pdb file has the following structure
> 
> ATOM 1 C ACE A 145 17.175 5.988 69.357 1.00 0.00 C
> ATOM 2 O ACE A 145 18.274 6.337 68.399 1.00 0.00 O
> ATOM 3 CA ACE A 145 17.256 4.596 68.703 1.00 0.00 C
> ATOM 4 N HIS A 146 16.165 6.227 70.468 1.00 44.68 N
> ATOM 5 CA HIS A 146 15.557 6.451 71.779 1.00 45.28 C
> ATOM 6 C HIS A 146 14.848 5.220 72.313 1.00 42.21 C
> ..
> 
> ATOM 65 ND2 ASN A 152 12.707 -14.633 75.307 1.00 42.30 N
> ATOM 66 N NH2 A 153 14.154 -16.823 71.228 1.00 0.00 N
> 
> For that I use the following command
> 
> pdb2gmx_mpi -f beta-I-Ac-NH2.pdb -o beta-I-Ac-NH2.gro -p 
> beta-I-Ac-NH2.top -ignh
> 
> I obtain the following error:
> 
> Fatal error:
> atom N not found in residue 1ACE while combining tdb and rtp
> 
> What is wrong since the N atom exists in the residu ACE in my pdb file
> 
> I have also read in the mailing list that the "-ter" argument can be use 
> to select the N and C term types
> 
> If i use the command
> 
> pdb2gmx_mpi -f beta-I-Ac-NH2.pdb -o beta-I-Ac-NH2.gro -p 
> beta-I-Ac-NH2.top -ignh -ter
> 
> i obtain an other message "Fatal error:
> Atom H not found in residue 9 while adding improper"
> 

What did you specify as your termini?  For capped groups, it should be "None," 
otherwise pdb2gmx will assign whatever other option you give it, -NH3+ or -NH2.

-Justin

> Thank you in advance for your help
> 
> Stefane
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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