[gmx-users] Azurin protein attached to metal atom of Cu.

[Justin Lemkul]

On 4/28/14, 9:14 AM, Alessia Giuliani wrote:
> Dear gromacs users,
>
>   I have a problem regarding the simulation of Azurin protein   attached to
> metal atom of
>   Cu. I edited the "aminoacids.rtp" file including CU as residue and i added
> the type of covalent bond that i need in the terminal part of ffbonded.it
> that regard  special bonds.
>   I have also added a line to "specbond.dat" regarding the SG-Cu
>   covalent bond. But while running the pdb2gmx command, (without any
>   error) it just adds a SG  with CU  and there is no
>   information on SG-CU bond in topology file. if I include it by hand,
> however, is ignored.

grompp doesn't pick and choose what to pay attention to.  Either there's a bond 
there or there's not.  You'll have to provide the actual relevant commands and 
topology snippets for anyone to make sense of what's going on here.  The 
specbond.dat approach should work, though.  If it's not creating a bond, then 
the distance criterion isn't set properly in specbond.dat.

>   it seems that the program creates a bridge between the atoms but with fixed
> distance.

I don't know what this means.  If a bond exists in the topology, it has to have 
parameters related to it.  If no such parameters exist, grompp will fail with a 
fatal error.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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