Re: [gmx-users] Atomtype 'sy' not found

[Mark Abraham]

Hi,

There's also atomtypes.atp file in force fields that perhaps you need to
adjust.

Mark

On Tue, Feb 13, 2018 at 10:40 AM  wrote:

>
> Hi all,
>
>I was trying to pass a file through GROMACS using following command:
>
> > $gmx grompp -f minim_gmx5.mdp -c Solv.gro -p topol.top -o ions.tpr
>
>   Then the follwing error popped up:
>
> > Atomtype sy not found
>
>   This is due to the presence of sulphur atom in my drug molecule
> Zafirlukast. I used AMBER beforehand to generate topologies for my
> molecule and this is the output under "atom" section:
>
> > ;name   bond_type mass charge   ptype   sigma
> > epsilon   Amb
> > sy   sy  0.0  0.0   A 3.56359e-01
> > 1.04600e+00 ; 2.00  0.2500
>
>Another additional information, I am using a customized version of
> force field in my work. So can I fix this problem by simply pasting
> this result into appropriate sections of my force field files? If that
> is the case, where should I paste or add them? If this information is
> insufficient to resolve this issue, does it means that I need to
> generate other parameters using some expert techniques that were far
> beyond for an undergraduate? Hope someone can answer my question,
> thank you in advance!
>
> Yours Sincerely,
> JZ
>
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[gmx-users] Atomtype 'sy' not found

[chaijz]

Hi all,

  I was trying to pass a file through GROMACS using following command:


$gmx grompp -f minim_gmx5.mdp -c Solv.gro -p topol.top -o ions.tpr


 Then the follwing error popped up:


Atomtype sy not found


 This is due to the presence of sulphur atom in my drug molecule  
Zafirlukast. I used AMBER beforehand to generate topologies for my  
molecule and this is the output under "atom" section:


;name   bond_type mass charge   ptype   sigma  
epsilon   Amb
sy   sy  0.0  0.0   A 3.56359e-01
1.04600e+00 ; 2.00  0.2500


  Another additional information, I am using a customized version of  
force field in my work. So can I fix this problem by simply pasting  
this result into appropriate sections of my force field files? If that  
is the case, where should I paste or add them? If this information is  
insufficient to resolve this issue, does it means that I need to  
generate other parameters using some expert techniques that were far  
beyond for an undergraduate? Hope someone can answer my question,  
thank you in advance!


Yours Sincerely,
JZ

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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[gmx-users] Atomtype sy not found error

[chaijz]

Hi all,

  I was trying to pass a file through GROMACS using following command:


$gmx grompp -f minim_gmx5.mdp -c Solv.gro -p topol.top -o ions.tpr


 Then the follwing error popped up:


Atomtype sy not found


 This is due to the presence of sulphur atom in my drug molecule  
Zafirlukast. I used AMBER beforehand to generate topologies for my  
molecule and this is the output under "atom" section:


;name   bond_type mass charge   ptype   sigma  
epsilon   Amb
sy   sy  0.0  0.0   A 3.56359e-01
1.04600e+00 ; 2.00  0.2500


  Another additional information, I am using a customized version of  
force field in my work. So can I fix this problem by simply pasting  
this result into appropriate sections of my force field files? If that  
is the case, where should I paste or add them? If this information is  
insufficient to resolve this issue, does it means that I need to  
generate other parameters using some expert techniques that were far  
beyond for an undergraduate? Hope someone can answer my question,  
thank you in advance!


Yours Sincerely,
JZ

--
Gromacs Users mailing list

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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