Re: [gmx-users] Unknown bond_atomtype when trying to use charm27 with cgenff

>FWIW, we have a complete CHARMM36 + latest CGenFF available at our website to >save you some pain: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs That looks helpful. Thanks. >So if it finds a bonded interaction that involves an atom type >it doesn't know about (e.g. you have a type in

Re: [gmx-users] Unknown bond_atomtype when trying to use charm27 with cgenff

On 11/26/16 2:41 PM, Jonathan Phillips wrote: Hi, I'm trying to run a simulation of a protein:ligand complex using chamm27 and cgenff2b7. After a little hacking (I'm using a PRES), I've used charmm2gromacs-pvm.py to convert cgenff2b7 to cgenff2b7.ff/, and then combined that with the charmm27

[gmx-users] Unknown bond_atomtype when trying to use charm27 with cgenff

Hi, I'm trying to run a simulation of a protein:ligand complex using chamm27 and cgenff2b7. After a little hacking (I'm using a PRES), I've used charmm2gromacs-pvm.py to convert cgenff2b7 to cgenff2b7.ff/, and then combined that with the charmm27 forcefield that comes with gromacs. pdb2gmx runs

Re: [gmx-users] Unknown bond_atomtype CAY

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Re: [gmx-users] Unknown bond_atomtype

Thanks Justin, I think that¹s everything I need to know. Kind regards Anthony Dr Anthony Nash Department of Chemistry University College London On 17/02/2016 22:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul"

Re: [gmx-users] Unknown bond_atomtype

On 2/17/16 5:11 PM, Nash, Anthony wrote: Hi, Thanks for the information, Mark. I fully parameterised the bonded terms using QM data and some software I wrote. Now that I’ve sorted out ffnonbonded [atomtypes], all that remains are some missing angle terms. I want to have the forcefield files

Re: [gmx-users] Unknown bond_atomtype

Hi, Thanks for the information, Mark. I fully parameterised the bonded terms using QM data and some software I wrote. Now that I’ve sorted out ffnonbonded [atomtypes], all that remains are some missing angle terms. I want to have the forcefield files correct so an MD simulation can be generated

Re: [gmx-users] Unknown bond_atomtype

Hi, Your MOD residues are LYS connected by a ring, so the atom types and bonds sections should be pretty much as for LYS, with the ring parts perhaps along the lines of TYR. If you have done a full parameterization somehow and have specialized atom types, then yes, those bonded and non-bonded

Re: [gmx-users] Unknown bond_atomtype

Dear Mark, I didn’t expect the problem was in ffnonbonded.itp. Problem solved. Thanks for the earlier hint. Anthony On 17/02/2016 18:01, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nash, Anthony"

Re: [gmx-users] Unknown bond_atomtype

Hi Mark, Further to my earlier email. I’ve answered the query as to whether atom types and names can be the same. This is fine, judging by The N N and O O in all of the amino acid types. I suspect I either have an additional problem or I have identified the root cause of my original problem.

Re: [gmx-users] Unknown bond_atomtype

Hi Mark, Thanks for the reply. I’m a little confused when you say “Choose existing types”. Are you saying that I am confined to only those atom types that come along with the forcefield upon installation, or that I can add new types but I’ve made a slight mishap between when specifying them

Re: [gmx-users] Unknown bond_atomtype

Hi, You've specified a type for your atom in [atoms] and elsewhere a bond that uses it. Grompp has to find parameters for a bond between those two types, etc. Choose existing types ;-) Mark On Wed, 17 Feb 2016 17:27 Nash, Anthony wrote: > Hi all, > > As per a previous email

[gmx-users] Unknown bond_atomtype

Hi all, As per a previous email (cross linking two peptide chains), I¹ve created a brand new crosslink (think disulphide bond) residue from scratch. I have defined it in all the files necessary (.rtp, residuetypes, specbond, atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no