On 7/18/12 5:58 AM, reising...@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)
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
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.
Use -ignh and pdb2gmx will rebuild all hydrogens for you.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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