[gmx-users] How to cap a peptide using pdb2gmx

[Justin A. Lemkul]

Camilo Andrés Jimenez Cruz wrote:
> Hi everybody
> 
> I downloaded a pdb entry from RCSB and it comes with charged terminii,
> for example, the first aminoacid is
> 
> 
> ATOM      1  N   ASN A   1      -8.901   4.127  -0.555  1.00  0.00           N
> ATOM      2  CA  ASN A   1      -8.608   3.135  -1.618  1.00  0.00           C
> ATOM      3  C   ASN A   1      -7.117   2.964  -1.897  1.00  0.00           C
> ATOM      4  O   ASN A   1      -6.634   1.849  -1.758  1.00  0.00           O
> ATOM      5  CB  ASN A   1      -9.437   3.396  -2.889  1.00  0.00           C
> ATOM      6  CG  ASN A   1     -10.915   3.130  -2.611  1.00  0.00           C
> ATOM      7  OD1 ASN A   1     -11.269   2.700  -1.524  1.00  0.00           O
> ATOM      8  ND2 ASN A   1     -11.806   3.406  -3.543  1.00  0.00           N
> ATOM      9  H1  ASN A   1      -8.330   3.957   0.261  1.00  0.00           H
> ATOM     10  H2  ASN A   1      -8.740   5.068  -0.889  1.00  0.00           H
> ATOM     11  H3  ASN A   1      -9.877   4.041  -0.293  1.00  0.00           H
> ATOM     12  HA  ASN A   1      -8.930   2.162  -1.239  1.00  0.00           H
> ATOM     13  HB2 ASN A   1      -9.310   4.417  -3.193  1.00  0.00           H
> ATOM     14  HB3 ASN A   1      -9.108   2.719  -3.679  1.00  0.00           H
> ATOM     15 HD21 ASN A   1     -11.572   3.791  -4.444  1.00  0.00           H
> ATOM     16 HD22 ASN A   1     -12.757   3.183  -3.294  1.00  0.00           H
> 
> and the same goes for the last one
> 
> I need to use ACE and NME for the terminii, so I tried using the -ter
> option in the pdb2gmx command, but when I use it it says
> N-terminus: none
> C-terminus: none
> and don't let me choose any terminii.
> 
> Any ideas.
> 

The coordinates for the cap must be present in the .pdb file.

-Justin

> Thanks in advance
> 
> --
> Camilo Andrés Jiménez Cruz
> 
> 
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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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