[gmx-users] problems with pdb2gmx
Mark.Abraham at anu.edu.au
Wed Jul 18 12:09:05 CEST 2012
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
> 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
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
> 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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