[gmx-users] Query

Justin Lemkul jalemkul at vt.edu
Wed Feb 12 14:45:40 CET 2020



On 2/11/20 4:46 PM, sai manohar wrote:
> You cannot generate the desired parameters (.itp) for metals in the ATB
> server. In fact even CGenFF or RED server are also not useful for metals.
> However, if you have access to any DFT modeling in house to perform QM
> calculations using Gaussian etc., you can generate/build your own force
> field for these particular kind of molecules.
>
> Hope that's helpful.

To add on to this, one would not parametrize ferric citrate, but would 
instead parametrize citrate (which CGenFF and other servers can handle) 
and Fe3+ separately (based on free energy of hydration or whatever other 
experimental data exist) and then verify that the interactions between 
the ion and relevant ligand and protein moieties is adequately described 
(against QM, usually).

-Justin

> On Tue, Feb 11, 2020, 18:23 Neha Tiwari <nt2614888 at gmail.com> wrote:
>
>> Dear Gromacs Experts,
>> I want to parametrize Ferric citrate and have already performed DFT
>> calculations using different basis sets, but I am unable to upload the
>> refined molecule on, ATB so that I can get its topology files to proceed
>> further.
>> Please help.
>>
>> Thanks in advance.
>> Neha.
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
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