[gmx-users] problems with pdb2gmx

[Mark Abraham]

On 18/07/2012 7:58 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> 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)

More particularly, you want no N terminus, since you are supplying it 
yourself. This may be the origin of your problem.

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

You can try hydrogen names like HH1 if the above doesn't work, but I 
believe GROMACS is trying to follow orders and use neutral termini. 
Reading and/or including the last fragment of the pdb2gmx output in your 
email would have been instructive.

You also need to get your C-terminus residue naming correct... e.g. CGLY 
for glycine.

Mark

>
>
>
> 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!!
>