[gmx-users] Adding Hydrogens by pdb2gmx

[Justin A. Lemkul]

James Starlight wrote:
> Justin,
> 
> Could you tell me more about adding caps by amber tools?
> 
> 1) I've found in that software ACE as well as other groups but they are 
> not standart
> 
> e.g ACE is below instead of simple CH3 group

ACE is an acetyl group, not a methyl.  Those coordinates look fine.

>              949 HH31 ACE    29       2.000   1.000  -0.000  1.00  0.00
> ATOM    950  CH3 ACE    29       2.000   2.090   0.000  1.00  0.00
> ATOM    951 HH32 ACE    29       1.486   2.454   0.890  1.00  0.00
> ATOM    952 HH33 ACE    29       1.486   2.454  -0.890  1.00  0.00
> ATOM    953  C   ACE    29       3.427   2.641  -0.000  1.00  0.00
> ATOM    954  O   ACE    29       4.391   1.877  -0.000  1.00  0.00
> ATOM    955  H7  ACE    29       3.582   3.629  -0.000  1.00  0.00
> 
> have you edited that group to standart form in amber tools or used 
> something else ?
> 
> 2) How you place CAP groups to desired coordinates?
> E.g if I use Edit- Unit Import Unit I can just import desired groups to 
> my pdb coordinates but how make linckage with N and C termi of my 
> molecule ? Or that linkage would be build by pdb2gmx -ter option ?
> 

You can draw them in xleap wherever you like.  There's likely tutorial material 
out there for such tings.

> 3) What another CAP groups in amber tools should I use for capping of 
> termi wich would be compatible with gromacs ff?
> 

ACE and NH2 are built in to Gromos96; they will work fine.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================