[gmx-users] problems with pdb2gmx

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Wed Jul 18 11:58:06 CEST 2012

Hi everybody,

I want to use pdb2gmx for my protein.
My protein has a ACE cap at one termini. And I looked it up in the
aminoacids.rtp file and there is also a ACE entry.

But still I get an error when using pdb2gmx

my command is like this:

pdb2gmx -f 3m71_hyd_cap.pdb -o 3m71.gro -p 3m71.top -ter -lys -arg -asp
-glu -his -water tip3p -ff amber03

I use it this why because I want to the residues to be protonated (-lys
-arg -asp -glu -his) and the termini shell be not charged (-ter)

My error is:

Atom HH1 in residue ACE 5 was not found in rtp entry ACE with 6 atoms
while sorting atoms.

I understand that there is a different between my ACE definition and the
one form gromacs.

The ACE in my file look like this:

ATOM      1  CH3 ACE     5     -15.187 -10.824 -17.012  1.00  0.00        
ATOM      2  C   ACE     5     -15.919 -10.927 -15.673  1.00  0.00        
ATOM      3  O   ACE     5     -15.898  -9.978 -14.893  1.00  0.00        
ATOM      4 1H   ACE     5     -14.703  -9.826 -17.094  1.00  0.00        
ATOM      5 2H   ACE     5     -14.413 -11.621 -17.076  1.00  0.00        
ATOM      6 3H   ACE     5     -15.914 -10.956 -17.845  1.00  0.00        

And the definition in gromacs looks like this:

[ ACE ]
 [ atoms ]
  HH31    HC           0.076010    1
   CH3    CT          -0.190264    2
  HH32    HC           0.076011    3
  HH33    HC           0.076010    4
     C    C            0.512403    5
     O    O           -0.550170    6
 [ bonds ]
  HH31   CH3
   CH3  HH32
   CH3  HH33
   CH3     C
     C     O
 [ impropers ]
   CH3    +N     C     O

The differ in the names of the hydrogen atoms.

So what can I do now that they are the same?

I already tried to name the ones in my pdb file like the ones in the rtp
file (HH33 instead of 3H). And I tried to name the hydrogens in the rtp
file like the ones in pdb file (H1 instead of HH31).

But nothing worked.

Thank you for your help!!

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