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

[Justin Lemkul]

On 2/14/20 6:09 AM, Atila Petrosian wrote:
> Dear Justin,
> Thanks for answer.
>
> You said " There is no reason to use this totally obsolete force field
> (ffgmx.itp)".
> I used ffgmx.itp, because there was a example.top file in Tieleman's web
> site:

That example is almost as old as I am :) It reproduces published work 
but no longer reflects the state of the art. ffgmx (the "GROMACS force 
field," which is a terrible name for a hacked/partially undocumented 
GROMOS87) is no longer acceptable for modern simulations. Please see a 
more updated approach that uses GROMOS96 at 
http://www.mdtutorials.com/gmx/membrane_protein/index.html though I will 
note that the Berger parameters that are distributed by Tieleman and 
used in that tutorial are also not as high-quality as other more modern 
parameter sets like Slipids and CHARMM36.

-Justin

> -------------------------------------------------------
> ; topology for 1 alm molecule, 128 popc lipids, water and 1 counter ion
> ; alm.itp can be made in a straightforward manner with pdb2gmx, starting
> ; with a pdb file of alamethicin.
> ; make sure lipid.itp, popc.itp and alm.itp are in a location where
> ; grompp can find them (GMXLIB, current directory, or directory given in
> ; the .mdp file with the include option.
> #include "ffgmx.itp"
> #include "lipid.itp"
> #include "popc.itp"
> #include "alm.itp"
> #include "ions.itp"
>
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
>
> [ system ]
> ; name
> Alm on surf + relaxed popc
>
> [ molecules ]
> ; name number
> Protein 1
> POPC    128
> SOL     3552
> Na      1
> -------------------------------------------------------
> Based on your suggestion, I used following in my topology file (I deleted
> ffgmx.itp):
>
> #include "lipid.itp"
> #include "dppc.itp"
> #include "lig.itp"
> -------------------------------------------------------
> But I encountered with:
> -------------------------------------------------------
> Fatal error:
> Syntax error - File lipid.itp, line 11
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
> -------------------------------------------------------
> lipid.itp file from Tieleman's web site is as follows:
> -------------------------------------------------------
> ;; this forcefield is a mixture of lipid and GROMOS parameters. GROMOS
> ;; parameters taken from ffgmxnb.itp, lipid parameters from Berger et
> ;; al, Biophys. J. 72, pp. 2002-2013. Parameters starting with L are
> ;; lipid parameter. LP2 and LP3 are Bergers pentadecane parameters,
> ;; the rest is OPLS. The lipids see SPC/SPCE, and lipids as
> ;; OPLS/Berger, protein as GROMOS, the protein sees lipids as GROMOS.
>
> [ defaults ]
> 1       1
>
> [ atomtypes ]
> ;name     mass     charge ptype  c6           c12
> ;
>     LO    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS
>    LOM    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS
>    LNL    14.0067    0.000  A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS
>     LC    12.0110    0.000  A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS
>    LH1    13.0190    0.000  A 4.03100e-03 1.21400e-05 ;CH1, OPLS
>    LH2    14.0270    0.000  A 7.00200e-03 2.48300e-05 ;CH2, OPLS
>     LP    30.9738    0.000  A 9.16000e-03 2.50700e-05 ;phosphor, OPLS
>    LOS    15.9994    0.000  A 2.56300e-03 1.86800e-06 ;ester oxygen, OPLS
>    LP2    14.0270    0.000  A 5.87400e-03 2.26500e-05 ;RB CH2, Bergers LJ
>    LP3    15.0350    0.000  A 8.77700e-03 3.38500e-05 ;RB CH3, Bergers LJ
>    LC3    15.0350    0.000  A 9.35700e-03 3.60900e-05 ;CH3, OPLS
>    LC2    14.0270    0.000  A 5.94700e-03 1.79000e-05 ;CH2, OPLS
>    -------------------------------------------------------
>
> How to resolve that?
>
> 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

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