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

[Nikolaos Michelarakis]

Dear Justin,

Thank you very much for your reply. I have tried the converter but I think
I don't have enough experience to get the CHARMM files working properly
with the converter. If I sent you the files, would it be possible to do it
for me or guide me through it?

Thanks again,

Nicholas


On 23 June 2014 17:42, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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