Re: [gmx-users] Unknown bond_atomtype CAY

2016-10-08 Thread Justin Lemkul
On 10/8/16 2:58 AM, Sameer Edirisinghe wrote: Dear gromacs users, Dr. Justin, I managed to run md simulation with the aid of your helps here . As the next step I'm trying to create a crystal from polymer molecule so i can put several molecules to the same box and do a simulation. What

Re: [gmx-users] Unknown bond_atomtype CAY

2016-10-08 Thread Sameer Edirisinghe
Dear gromacs users, Dr. Justin, I managed to run md simulation with the aid of your helps here . As the next step I'm trying to create a crystal from polymer molecule so i can put several molecules to the same box and do a simulation. What approach should I take here ? Regards Sameera

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-21 Thread Justin Lemkul
On 9/21/16 7:42 AM, Sameer Edirisinghe wrote: Dear Dr. Justin, Thanks for the explanation. Now i got the point you mentioned here. Then i checked the bonds i have mentioned in .rtp file and then i found the relevant bonded type. then i checked the ffbonded.itp file and i found that bond type

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-21 Thread Sameer Edirisinghe
Dear Dr. Justin, Thanks for the explanation. Now i got the point you mentioned here. Then i checked the bonds i have mentioned in .rtp file and then i found the relevant bonded type. then i checked the ffbonded.itp file and i found that bond type is already in there. As an example, CAY HA1 ;

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-20 Thread Justin Lemkul
On 9/20/16 8:27 AM, Sameer Edirisinghe wrote: Dear Dr. Justin, Thanks for the all valuable points here. Please see the below sample bonds i defined in .rtp file. how to define bond type for them ? i know oplsaa atom type of each of them. what i dont understand in how to add them to

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-20 Thread Sameer Edirisinghe
Dear Dr. Justin, Thanks for the all valuable points here. Please see the below sample bonds i defined in .rtp file. how to define bond type for them ? i know oplsaa atom type of each of them. what i dont understand in how to add them to ffbonded.itp file. these bonds are general bonds such as C-C

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-19 Thread Justin Lemkul
On 9/18/16 10:14 PM, Sameer Edirisinghe wrote: Dear Dr. Justin, If the bond types have not added, following errors occuring with grompp, 1) ERROR 1 [file topol.top, line 108]: No default Bond types 2) ERROR 2 [file topol.top, line 168]: No default Angle types 3) ERROR 3 [file

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-18 Thread Sameer Edirisinghe
Dear Dr. Justin, If the bond types have not added, following errors occuring with grompp, 1) ERROR 1 [file topol.top, line 108]: No default Bond types 2) ERROR 2 [file topol.top, line 168]: No default Angle types 3) ERROR 3 [file topol.top, line 426]: No default Ryckaert-Bell. types

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-18 Thread Justin Lemkul
On 9/18/16 2:26 PM, Sameer Edirisinghe wrote: Dear Dr. Justin, Now i can understand what what i have mistaken there. How can i derive [bondtypes] for bonds i have used in .rtp file ? Determine if you need to in the first place. If grompp gives you errors about missing parameters, first

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-18 Thread Sameer Edirisinghe
Dear Dr. Justin, Now i can understand what what i have mistaken there. How can i derive [bondtypes] for bonds i have used in .rtp file ? Regards On Sun, Sep 18, 2016 at 11:38 PM, Justin Lemkul wrote: > > > On 9/18/16 2:06 PM, Sameer Edirisinghe wrote: > >> Dear Dr. Justin,

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-18 Thread Justin Lemkul
On 9/18/16 2:06 PM, Sameer Edirisinghe wrote: Dear Dr. Justin, If atom names names cant use in ffbonded.itp file how should i add bond interaction used in .rtp file to ff..itp file ? this is the part i dont understand. Do i need to modify ffnonbonded.itp file to correct the "Unknown

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-18 Thread Sameer Edirisinghe
Dear Dr. Justin, If atom names names cant use in ffbonded.itp file how should i add bond interaction used in .rtp file to ff..itp file ? this is the part i dont understand. Do i need to modify ffnonbonded.itp file to correct the "Unknown bond_atomtype' error which occurring while runing grompp

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-18 Thread Justin Lemkul
On 9/18/16 1:12 PM, Sameer Edirisinghe wrote: Dear Dr. Justin, Thanks for the reply. Following is the whole .rtp file i used. ( As you said it was generated by using PRODRG) You shouldn't use the charges from PRODRG. They assume a united-atom force field, and are of very low quality.

Re: [gmx-users] Unknown bond_atomtype CAY

2016-09-18 Thread Justin Lemkul
On 9/18/16 12:30 PM, Sameer Edirisinghe wrote: Dear users, There is one thing i cannot clarify from gromacs manual which is about following error occurred while running grompp Fatal error: Unknown bond_atomtype CAY I used to create .rtp file from atom types which are already defined in

[gmx-users] Unknown bond_atomtype CAY

2016-09-18 Thread Sameer Edirisinghe
Dear users, There is one thing i cannot clarify from gromacs manual which is about following error occurred while running grompp Fatal error: Unknown bond_atomtype CAY I used to create .rtp file from atom types which are already defined in atomtype.atp file. But still above error occurring