[gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

[Justin Lemkul]

On 6/23/14, 9:48 AM, Nikolaos Michelarakis wrote:
> Dear All,
>
> First, I would like to say that I have started using GROMACS during this
> last month so please take that in mind when answering.
>
> I am trying to run an MD simulation of an enzyme which contains some non
> standard residues such as a tungsten metal ion and some other cofactors. I
> understand that I need to create the topology and find the parameters for
> these non-standard residues. Reading the manual I saw about .itp files and,
> correct me if I'm wrong, but it's my understanding that these are used for
> parts of the topology which are not bonded or intergrated in the structure
> that is being simulated. My question is how do I include these bonded parts
> in the simulation?
>

An .itp file specifies a distinct [moleculetype] that shares no bonded 
interactions with any other species in the system.  The development version of 
the code has the capability to do intermolecular bondeds, but at present the 
distinction is true enough.  Are you asking how to include actual bonds between 
your non-standard residues and other parts of the system?  If so, then the only 
options are:

1. Create an .rtp entry for your non-standard residue(s) and modify specbond.dat 
accordingly, as these will likely be non-linear bonds.  That way, you'll have a 
single [moleculetype] in which you will have bonds between the different residues.

2. Use git to obtain the developmental version of the code that has 
intermolecular bond capabilities.  I don't recall offhand which patch has it or 
if it's even been merged, but it's in the Gerrit repo, at least.

> My second question, someone has already developed a topology and some
> parameters for this structure but in CHARM. I tried using one of the two
> scripts available online to convert them to GROMACS but to no avail. Is
> there a way to automatically do this or will I have to go all over it by
> hand?
>

If you have a stream file, we have a converter:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

It was designed to interface with CGenFF .str files from ParamChem, but it 
should do the job.

-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

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