[gmx-users] grompp error : Atomtype CAro not found

Justin Lemkul jalemkul at vt.edu
Mon Mar 2 14:45:21 CET 2020



On 3/2/20 2:40 AM, Atila Petrosian wrote:
> Hi Dallas,
> thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB
> server.
>
> My system contains lipid molecules and small molecule. For lipid molecules,
> Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both
> of gromos54a7_atb.ff

I explicitly do not endorse/suggest the force field combination, as 
noted on the home page of that tutorial:

"*Please note*that the purpose of this tutorial is instructional, to 
build a membrane protein system and also to understand GROMACS force 
field organization and methods for modification. *This tutorial is not 
an endorsement or suggestion that you use these specific parameters for 
your simulation.* The approach taken here works well in the case where 
one needs to augment a parameter set with other parameters that have 
been derived in a consistent manner."

http://www.mdtutorials.com/gmx/membrane_protein/index.html

But in any event, the logic is the same if you need to augment any force 
field with new parameters (that are compatible with the parent force 
field). There are far better options for lipids than the old Berger 
parameters used in the tutorial. I wrote the tutorial in 2008 and it 
reflected a common protocol at the time. I have acknowledged within the 
tutorial that the force field and methods used are somewhat outdated but 
that the logic of extending a force field and using the tutorial as a 
vehicle to understand GROMACS force field organization remains valuable.

-Justin

> and  gromos53a6_lipid.ff in topology file.
>
> Please guide me.
>
> Best,
> Atila

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

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
http://www.thelemkullab.com

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