[gmx-users] grompp error : Atomtype CAro not found
Dallas Warren
dallas.warren at monash.edu
Sun Mar 1 23:05:50 CET 2020
Did you read what the ATB told you about the topologies it generates, and
what forcefield you have to use? There is a warning posted on the page
where you download your topology files that applies directly to this error
you have encountered:
"*Warning!* This molecule contains non-standard atom types not included in
the standard GROMOS 54A7 forcefield. To use these atom types the internal
GROMACS parameter files must be updated. These can be downloaded using the
link below. Instructions on where to place (and how to use) the files are
provided in the README file included in the archive."
ATB uses GROMOS 54a7 ATB, and you have to download and use that forcefield
for any molecules you generate using that server. You cannot just mix it
with GROMOS 53a6 like you have tried to, since 54a7_atb has additional atom
types.
Stick with a single forcefield, do not mix then because the vast majority
are not compatible in that manner.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.
On Sun, 1 Mar 2020 at 19:41, Atila Petrosian <atila.petrosian at gmail.com>
wrote:
> Hi gromacs users,
>
> I am doing MD simulation of my system (DPPC lipid + 2 drug molecules +
> water molecules) using gromacs 2019.
>
> I used ATB for drug molecules and Membrane Protein: KALP15 in DPPC
> gromacs tutorial method for lipid molecules (based on Justin Lemkul
> suggestion in my previous post:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2020-February/128420.html
> ).
>
> ---------------------------------------
> My topology file is as follows:
> ---------------------------------------
> ; Include forcefield parameters
> #include "gromos53a6_lipid.ff/forcefield.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include DPPC chain topology
> #include "dppc.itp"
>
> ; Include drug topology
> #include "lig.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> [ system ]
> ; Name
> dopc/lig/sol in water
>
> [ molecules ]
> ; Compound #mols
> DPPC 128
> LIG 2
> SOL 8257
> ---------------------------------------
> My lig.itp file is as follows:
> ---------------------------------------
> .
> .
> ;
> [ moleculetype ]
> ; Name nrexcl
> LIG 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 HC 1 LIG H27 1 0.131 1.0080
> 2 CAro 1 LIG C24 2 -0.130 12.0110
> 3 CAro 1 LIG C23 3 -0.130 12.0110
> 4 HC 1 LIG H26 4 0.131 1.0080
> 5 CAro 1 LIG C22 5 -0.119 12.0110
> 6 HC 1 LIG H25 6 0.135 1.0080
> 7 CAro 1 LIG C21 7 -0.039 12.0110
> 8 CAro 1 LIG C26 8 -0.119 12.0110
> 9 HC 1 LIG H29 9 0.135 1.0080
> 10 CAro 1 LIG C25 10 -0.130 12.0110
> 11 HC 1 LIG H28 11 0.131 1.0080
> 12 C 1 LIG C18 12 -0.051 12.0110
> 13 CH2 1 LIG C19 13 0.055 14.0270
> 14 CH3 1 LIG C20 14 0.020 15.0350
> 15 CAro 1 LIG C11 15 -0.025 12.0110
> 16 CAro 1 LIG C12 16 -0.040 12.0110
> 17 CAro 1 LIG C13 17 -0.117 12.0110
> 18 HC 1 LIG H15 18 0.137 1.0080
> 19 CAro 1 LIG C14 19 -0.133 12.0110
> 20 HC 1 LIG H16 20 0.131 1.0080
> 21 CAro 1 LIG C15 21 -0.129 12.0110
> 22 HC 1 LIG H17 22 0.131 1.0080
> 23 CAro 1 LIG C16 23 -0.133 12.0110
> 24 HC 1 LIG H18 24 0.131 1.0080
> 25 CAro 1 LIG C17 25 -0.117 12.0110
> 26 HC 1 LIG H19 26 0.137 1.0080
> 27 CAro 1 LIG C8 27 -0.076 12.0110
> 28 CAro 1 LIG C7 28 -0.079 12.0110
> 29 HC 1 LIG H12 29 0.139 1.0080
> 30 CAro 1 LIG C6 30 -0.184 12.0110
> 31 HC 1 LIG H11 31 0.143 1.0080
> 32 CAro 1 LIG C5 32 0.087 12.0110
> 33 CAro 1 LIG C10 33 -0.184 12.0110
> 34 HC 1 LIG H14 34 0.143 1.0080
> 35 CAro 1 LIG C9 35 -0.079 12.0110
> 36 HC 1 LIG H13 36 0.139 1.0080
> 37 OE 1 LIG O1 37 -0.219 15.9994
> 38 CH2 1 LIG C4 38 0.149 14.0270
> 39 CH2 1 LIG C3 39 0.101 14.0270
> 40 NTer 1 LIG N1 40 -0.267 14.0067
> 41 CH3 1 LIG C1 41 0.097 15.0350
> 42 CH3 1 LIG C2 42 0.097 15.0350
> ; total charge of the molecule: 0.000
> [ bonds ]
> ; ai aj funct c0 c1
> 1 2 2 0.1090 1.2300e+07
> 2 3 2 0.1390 8.6600e+06
> .
> .
> .
> ---------------------------------------
> After using command: gmx grompp -f em1.mdp -c system.gro -p topol.top -o
> em1.tpr,
> I encountered with the following error:
> ---------------------------------------
> ERROR 1 [file lig.itp, line 66]:
> Atomtype CAro not found
> ---------------------------------------
> How to resole it?
>
> Best,
> Atila
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