[gmx-users] energy minimization

[farial tavakoli]

Dear Justin 

I used LigParGen server to generate ligand topology but I dont know what changes I have to do in .itp file. 
 when I issued this command:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor 

faced this error:ERROR 1 [file LIG.itp, line 11]:
  Atomtype opls_800 not found
I checked the aminoacids.rtp file  of  /usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not atomtype opls_800 and 801 and ... in this file. while the LIG.itp which generated by LigParGen server has atomtype opls_800 , 801 and ... . 
I have to modify all of these atomtype opls_ in order to correspond to with aminoacid.rtp file? 
I would be thankfull if you help me.
bestFraial


   On Monday, July 16, 2018, 5:29:17 PM GMT+4:30, Justin Lemkul <jalemkul at vt.edu> wrote:  
 
 

On 7/16/18 3:49 AM, farial tavakoli wrote:
>  Dear Justin
>
> Thank you for your reply
> I noticed my problem ( the reason was topolgen.pl name in my directory, it is named topologen_1.1.pl in the working directory)
> I generated my ligand topology but got this :
> No output type specified. Using default type of .top
> Unknown atom type: N 13 with 2 bonds - cannot assign atom type.
> Using default H type for atom 16.
> Using default H type for atom 26.
> Using default H type for atom 31.
> Using default H type for atom 38.
> Using default H type for atom 39.
> Using default H type for atom 40.
> Using default H type for atom 41.
> Unknown atom type: N 42 with 2 bonds - cannot assign atom type.
> Using default H type for atom 47.
> Using default H type for atom 48.
> Using default H type for atom 49.
> Using default H type for atom 50.
> Using default H type for atom 51.
> Using default H type for atom 52.
>
> ********************************************************
> WARNING: Net charge on the molecule is -2.781
> You will need to make corrections to the output topology
> ********************************************************
>
> TopolGen, version 1.1_dev (10/14/2009) complete.
>
> Output topology has been written. An attempt has been made to assign charges and atom types based
> on existing functional groups, but they may not be correct.  No charge calculations or other
> parameterization calculations have been done.  Guesses have been made for charge groups.  Please
> inspect and correct the topology before using it in any simulations.  The author of the script does
> NOT guarantee accuracy or usability of any of the content; TopolGen was written as a convenience
> for outputting a skeleton topology, and nothing more.

Heed the above warning. TopolGen assigns parameters based on similarity 
to known functional groups. If your molecule has something unusual, it 
makes no attempt to try to assign reasonable parameters. You'll need to 
actually parametrize the molecule. Make use of available web servers 
like LikeParGen or others.

-Justin

>
> the N13 atom connected to C with double bond. it sounds topolgen can not identify N atom in 2 bonds with C .
> would you please help me to figure out this problem
> thans in advanceFarial
>
>      On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul <jalemkul at vt.edu> wrote:
>  
>  
>
> On 7/15/18 1:38 AM, farial tavakoli wrote:
>>    Dear Justin
>>
>> But I copied & pasted topolgen and perl5 folders in the working directory. and faced the mentioned error.
>>
>> Can't open perl script "topolgen.pl": No such file or directory
>> I dont know how I should figure out this problem.
> The problem is still the same: there's nothing called "topolgen.pl" in
> the working directory. List your files, you'll see it's called something
> else.
>
>> Which one of all-atom force fields will you choose to run a simulation on a complex with small molecule, if you want to calculate binding energy using G_MMPBSA ?I really need your guidance .
> Presumably any of them, but I don't do such calculations.
>
> -Justin
>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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