subject:"\[gmx\-users\] Unknown bond

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

2016-11-27 Thread Jonathan Phillips

>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 ffbonded.itp but not
>ffnonbonded.itp, which I bet is the case here) you get a fatal error.

Got it!  It's a little more subtle that that though.

forcefield.itp has
>#include "ffcgenbonded.itp"
>#include "ffcgennonbonded.itp"
so it's loading the bonded parameters before the non-bonded, it needs
to be the other way around.  I'd never have worked that out on my own.

Now to fix the next error.


Thanks for the help!

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

2016-11-26 Thread Justin Lemkul

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 forcefield that comes with gromacs.

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

pdb2gmx runs without error, however when I run grompp, I get this:

Program grompp, VERSION 5.0.4
Source code file:

/var/tmp/portage/sci-chemistry/gromacs-5.0.4/work/gromacs-5.0.4/src/gromacs/gmxpreprocess/toppush.c,
line: 742

Fatal error:
Unknown bond_atomtype CG1N1

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I can't work out what bond_atomtype is, or exactly where I've been stupid.

"bond_atomtype" means "an atom type used in a bonded interaction."

I've checked that:

atomtypes.atp contains the following line

CG1N1 12.01100 ; for cyano group

(if it's relevant, this was generated by appending the cgen atomtypes file
to the charmm atomtypes file).

ffcgenbonded.itp contains the following lines (under the [ bondtypes ]
section)

CG1N1 CG2R61 1 0.1435 288696.0
CG1N1 CG331 1 0.147 334720.0
CG1N1 NG1T1 1 0.118 881150.4

charmm27cgen.ff/forcefield.itp contains

#include "ffcgenbonded.itp"

topol.top contains

#include "./charmm27cgen.ff/forcefield.itp"

grompp is being called with -p topol.top

All bonds containing a CG1N1 atom in cgen.rtp are to one of the three
atomtypes in ffcgenbonded.itp quoted above.

Also, my ligand doesn't contain residues that have a CG1N1 atom in them
(neither does my protein, surprise, surprise).

So I don't know why it's looking at CG1N1, and I don't know why there are
issues with this atomtype, and I don't know what a bond_atomtype is, which
leaves me rather stuck.

Does anybody have any suggestions?

The presence of an atom type in the .atp file is not enough. That file is only
ever read by pdb2gmx. grompp needs parameters for all those atom types in
ffnonbonded.itp. So if it finds a bonded interaction that involves an atom type
it doesn't know about (e.g. you have a type in ffbonded.itp but not
ffnonbonded.itp, which I bet is the case here) you get a fatal error.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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

2016-11-26 Thread Jonathan Phillips

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 without error, however when I run grompp, I get this:

>Program grompp, VERSION 5.0.4
>Source code file:
/var/tmp/portage/sci-chemistry/gromacs-5.0.4/work/gromacs-5.0.4/src/gromacs/gmxpreprocess/toppush.c,
line: 742
>
>Fatal error:
>Unknown bond_atomtype CG1N1
>
>For more information and tips for troubleshooting, please check the GROMACS
>website at http://www.gromacs.org/Documentation/Errors

I can't work out what bond_atomtype is, or exactly where I've been stupid.

I've checked that:

atomtypes.atp contains the following line
>CG1N1   12.01100 ;  for cyano group
(if it's relevant, this was generated by appending the cgen atomtypes file
to the charmm atomtypes file).

ffcgenbonded.itp contains the following lines (under the [ bondtypes ]
section)
>CG1N1   CG2R61  1   0.1435  288696.0
>CG1N1   CG331   1   0.147   334720.0
>CG1N1   NG1T1   1   0.118   881150.4

charmm27cgen.ff/forcefield.itp contains
>#include "ffcgenbonded.itp"
topol.top contains
>#include "./charmm27cgen.ff/forcefield.itp"
grompp is being called with -p topol.top

All bonds containing a CG1N1 atom in cgen.rtp are to one of the three
atomtypes in ffcgenbonded.itp quoted above.

Also, my ligand doesn't contain residues that have a CG1N1 atom in them
(neither does my protein, surprise, surprise).

So I don't know why it's looking at CG1N1, and I don't know why there are
issues with this atomtype, and I don't know what a bond_atomtype is, which
leaves me rather stuck.

Does anybody have any suggestions?
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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 approach should
I take here ?



gmx genconf, gmx insert-molecules, etc.  See the manual.

If you're going to start doing something different, please start a new thread 
rather than dig up an old one that's not really related.


-Justin


Regards
Sameera Edirisinghe

On Sep 22, 2016 00:41, "Justin Lemkul"  wrote:




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 is already in there.
As an example,

CAY  HA1 ; this is one of bond i have in .rtp file. and for that bond,
relevant bond type (mentioned as below) was already in ffbonded.itp file
CTHC  10.10900   284512.0

But still following error is occurring while running 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

How do i refer particular bond types in ffbonded.itp file to my current
.gro file or any other relevant file ?



grompp won't complain about parameters being missing if they're actually
there. You're probably looking at the wrong line.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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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 Edirisinghe

On Sep 22, 2016 00:41, "Justin Lemkul"  wrote:

>
>
> 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 is already in there.
>> As an example,
>>
>> CAY  HA1 ; this is one of bond i have in .rtp file. and for that bond,
>> relevant bond type (mentioned as below) was already in ffbonded.itp file
>> CTHC  10.10900   284512.0
>>
>> But still following error is occurring while running 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
>>
>> How do i refer particular bond types in ffbonded.itp file to my current
>> .gro file or any other relevant file ?
>>
>>
> grompp won't complain about parameters being missing if they're actually
> there. You're probably looking at the wrong line.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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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 is already in there.
As an example,

CAY  HA1 ; this is one of bond i have in .rtp file. and for that bond,
relevant bond type (mentioned as below) was already in ffbonded.itp file
CTHC  10.10900   284512.0

But still following error is occurring while running 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

How do i refer particular bond types in ffbonded.itp file to my current
.gro file or any other relevant file ?



grompp won't complain about parameters being missing if they're actually there. 
You're probably looking at the wrong line.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

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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 ; this is one of bond i have in .rtp file. and for that bond,
relevant bond type (mentioned as below) was already in ffbonded.itp file
CTHC  10.10900   284512.0

But still following error is occurring while running 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

How do i refer particular bond types in ffbonded.itp file to my current
.gro file or any other relevant file ?

regards

On Tue, Sep 20, 2016 at 9:28 PM, Justin Lemkul  wrote:

>
>
> 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
>> ffbonded.itp file. these bonds are general bonds such as C-C , C-H C-O
>> bonds. 1) I dont understand how to define them in ffbonded.itp file.
>>
>>
> Look at ffnonbonded.itp.  The first column is the opls_* type.  The second
> column is the corresponding bonded type.  The bonded types are what you use.
>
> 2) what is the nomenclature/type which used in  ffbonded.itp file  to
>> define atoms (i.e. OWHW , OWLP, C_2   C3 , C CA ) ?
>>
>>
> These are the types listed in the second column of ffnonbonded.itp.
>
> 3) Do i need to define bonds in and atom in .rtp file and .pdb file using
>> above nomenclature/type ?
>>
>>
> The .rtp names must match the PDB atom names.  The [atoms] section of an
> .rtp entry defines a given atom's name, type, charge, and charge group.
> All remaining bonded interactions in an .rtp entry are defined using name
> only.
>
> -Justin
>
>
> Regards
>>
>>
>>
>> On Tue, Sep 20, 2016 at 12:59 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> 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 topol.top, line 426]:
   No default Ryckaert-Bell. types

 Atom types are seems to be correct as i derived them from atomtype.atp
 file.

 If the interaction don't cover by the force field, how can I define them
 in
 ffbonded.itp file ?


 See the manual.  Use atom types, not names.  If you're adding
>>> parameters,
>>> be sure they've been derived properly.  If you're still using anything
>>> from
>>> that PRODRG topology and trying to force it into OPLS-AA, don't.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> 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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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
ffbonded.itp file. these bonds are general bonds such as C-C , C-H C-O
bonds. 1) I dont understand how to define them in ffbonded.itp file.



Look at ffnonbonded.itp.  The first column is the opls_* type.  The second 
column is the corresponding bonded type.  The bonded types are what you use.



2) what is the nomenclature/type which used in  ffbonded.itp file  to
define atoms (i.e. OWHW , OWLP, C_2   C3 , C CA ) ?



These are the types listed in the second column of ffnonbonded.itp.


3) Do i need to define bonds in and atom in .rtp file and .pdb file using
above nomenclature/type ?



The .rtp names must match the PDB atom names.  The [atoms] section of an .rtp 
entry defines a given atom's name, type, charge, and charge group.  All 
remaining bonded interactions in an .rtp entry are defined using name only.


-Justin


Regards



On Tue, Sep 20, 2016 at 12:59 AM, Justin Lemkul  wrote:




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 topol.top, line 426]:
  No default Ryckaert-Bell. types

Atom types are seems to be correct as i derived them from atomtype.atp
file.

If the interaction don't cover by the force field, how can I define them
in
ffbonded.itp file ?



See the manual.  Use atom types, not names.  If you're adding parameters,
be sure they've been derived properly.  If you're still using anything from
that PRODRG topology and trying to force it into OPLS-AA, don't.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

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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 , C-H C-O
bonds. 1) I dont understand how to define them in ffbonded.itp file.

2) what is the nomenclature/type which used in  ffbonded.itp file  to
define atoms (i.e. OWHW , OWLP, C_2   C3 , C CA ) ?

3) Do i need to define bonds in and atom in .rtp file and .pdb file using
above nomenclature/type ?

Regards

On Tue, Sep 20, 2016 at 12:59 AM, Justin Lemkul  wrote:

>
>
> 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 topol.top, line 426]:
>>   No default Ryckaert-Bell. types
>>
>> Atom types are seems to be correct as i derived them from atomtype.atp
>> file.
>>
>> If the interaction don't cover by the force field, how can I define them
>> in
>> ffbonded.itp file ?
>>
>>
> See the manual.  Use atom types, not names.  If you're adding parameters,
> be sure they've been derived properly.  If you're still using anything from
> that PRODRG topology and trying to force it into OPLS-AA, don't.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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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 topol.top, line 426]:
  No default Ryckaert-Bell. types

Atom types are seems to be correct as i derived them from atomtype.atp
file.

If the interaction don't cover by the force field, how can I define them in
ffbonded.itp file ?



See the manual.  Use atom types, not names.  If you're adding parameters, be 
sure they've been derived properly.  If you're still using anything from that 
PRODRG topology and trying to force it into OPLS-AA, don't.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

Atom types are seems to be correct as i derived them from atomtype.atp
file.

If the interaction don't cover by the force field, how can I define them in
ffbonded.itp file ?

Regards

On Sep 19, 2016 3:57 AM, "Justin Lemkul"  wrote:

>
>
> 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 verify that your choice of atom types is
> correct. Then, if there are in fact interactions that the force field
> doesn't cover:
>
> 1. Make sure your choice of force field was appropriate
> 2. Parametrize them in a manner consistent with the parent force field
>
> -Justin
>
> 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,

 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 ?  If so how i
 should modify ffnonbonded.itp (I have attached my .rtp file herewith)


 You do not need to modify ffnonbonded.itp.
>>>
>>> You added an atom name in ffbonded.itp - this makes no sense and you
>>> cannot do it.  Bonded and nonbonded interactions are defined by type.
>>>
>>> You must use atom names only in .rtp files, because the .rtp entry tells
>>> pdb2gmx which atoms are bonded, and how.  You can't do that by type
>>> because
>>> that is not a unique way to identify connectivity.  The list of [bonds]
>>> in
>>> the .rtp just tells pdb2gmx which atoms are connect, it is separate from
>>> a
>>> [bondtypes] directive, which says what parameters are assigned to each
>>> interaction type.
>>>
>>> -Justin
>>>
>>>
>>>
>>> Regards
 Sameera

 On Sun, Sep 18, 2016 at 10:45 PM, Justin Lemkul 
 wrote:



> 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.  You can't force them into
> working with OPLS-AA.  It's fundamentally wrong.
>
> If you want free help with a problem, you have to provide full
> information. Fragments of .rtp files are not helpful and it's a waste
> of
> time for those who are trying to give you advice.
>
>
> [ bondedtypes ]
>
> ; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14
>> RemoveDih
>>   1  1   3  1
>>
>> ; MDI
>> [ MD ]
>>  [ atoms ]
>> CAY opls_135 0 1
>> CAX opls_135 0.048 2
>> CAW opls_135 0.047 2
>> CAV opls_135 0.144 2
>> OAU opls_154 -0.112 2
>> CAS opls_131 0.219 2
>> OAT opls_236 -0.41 2
>> NAO opls_900 0.073 2
>> HAO opls_250 -0.009 2
>> CAE opls_260 0.056 3
>> CAF opls_145 -0.018 3
>> HAF opls_140 0.004 3
>> CAA opls_145 -0.018 3
>> HAA opls_140 0.004 3
>> CAD opls_145 -0.018 3
>> HAD opls_140 0.004 3
>> CAC opls_145 -0.018 3
>> HAC opls_140 0.004 3
>> CAB opls_145 -0.022 4
>> CAG opls_071 0.044 4
>> CAH opls_145 -0.022 4
>> CAM opls_145 -0.008 5
>> HAM opls_140 0.008 5
>> CAL opls_145 -0.008 6
>> HAL opls_140 0.008 6
>> CAI opls_145 -0.008 7
>> HAI opls_140 0.008 7
>> CAJ opls_145 -0.008 8
>> HAJ opls_140 0.008 8
>> CAK opls_145 0.072 9
>> NAN opls_900 0.072 9
>> HAN opls_250 -0.009 9
>> CAP opls_131 0.214 9
>> OAQ opls_236 -0.419 9
>> OAR opls_154 -0.115 9
>> CAZ opls_135 0.14 9
>> CBA opls_135 0.045 9
>> CBB opls_135 0.01 10
>> CBC opls_135 -0.01 10
>> HA1 opls_140 -0.013 1
>> HA2 opls_140 -0.013 1
>> HA3 opls_140 -0.014 1
>> HAZ opls_140 -0.013 1
>> HA0 opls_140 -0.013 1
>> HAX opls_140 -0.013 1
>> HAY opls_140 -0.013 1
>> HAV opls_140 -0.013 1
>> HAW opls_140 -0.013 1
>> HAG opls_140 -0.013 1
>> HAH opls_140 -0.013 1
>> HA4 opls_140 -0.013 1
>> HA5 opls_140 -0.013 1
>> HBA opls_140 -0.013 1
>> HBB opls_140 -0.013 1
>> HBC opls_140 -0.013 1
>> HBD opls_140 -0.013

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 verify that your choice of atom types is correct. 
Then, if there are in fact interactions that the force field doesn't cover:


1. Make sure your choice of force field was appropriate
2. Parametrize them in a manner consistent with the parent force field

-Justin


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,

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 ?  If so how i
should modify ffnonbonded.itp (I have attached my .rtp file herewith)



You do not need to modify ffnonbonded.itp.

You added an atom name in ffbonded.itp - this makes no sense and you
cannot do it.  Bonded and nonbonded interactions are defined by type.

You must use atom names only in .rtp files, because the .rtp entry tells
pdb2gmx which atoms are bonded, and how.  You can't do that by type because
that is not a unique way to identify connectivity.  The list of [bonds] in
the .rtp just tells pdb2gmx which atoms are connect, it is separate from a
[bondtypes] directive, which says what parameters are assigned to each
interaction type.

-Justin




Regards
Sameera

On Sun, Sep 18, 2016 at 10:45 PM, Justin Lemkul  wrote:




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.  You can't force them into
working with OPLS-AA.  It's fundamentally wrong.

If you want free help with a problem, you have to provide full
information. Fragments of .rtp files are not helpful and it's a waste of
time for those who are trying to give you advice.


[ bondedtypes ]


; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14
RemoveDih
  1  1   3  1

; MDI
[ MD ]
 [ atoms ]
CAY opls_135 0 1
CAX opls_135 0.048 2
CAW opls_135 0.047 2
CAV opls_135 0.144 2
OAU opls_154 -0.112 2
CAS opls_131 0.219 2
OAT opls_236 -0.41 2
NAO opls_900 0.073 2
HAO opls_250 -0.009 2
CAE opls_260 0.056 3
CAF opls_145 -0.018 3
HAF opls_140 0.004 3
CAA opls_145 -0.018 3
HAA opls_140 0.004 3
CAD opls_145 -0.018 3
HAD opls_140 0.004 3
CAC opls_145 -0.018 3
HAC opls_140 0.004 3
CAB opls_145 -0.022 4
CAG opls_071 0.044 4
CAH opls_145 -0.022 4
CAM opls_145 -0.008 5
HAM opls_140 0.008 5
CAL opls_145 -0.008 6
HAL opls_140 0.008 6
CAI opls_145 -0.008 7
HAI opls_140 0.008 7
CAJ opls_145 -0.008 8
HAJ opls_140 0.008 8
CAK opls_145 0.072 9
NAN opls_900 0.072 9
HAN opls_250 -0.009 9
CAP opls_131 0.214 9
OAQ opls_236 -0.419 9
OAR opls_154 -0.115 9
CAZ opls_135 0.14 9
CBA opls_135 0.045 9
CBB opls_135 0.01 10
CBC opls_135 -0.01 10
HA1 opls_140 -0.013 1
HA2 opls_140 -0.013 1
HA3 opls_140 -0.014 1
HAZ opls_140 -0.013 1
HA0 opls_140 -0.013 1
HAX opls_140 -0.013 1
HAY opls_140 -0.013 1
HAV opls_140 -0.013 1
HAW opls_140 -0.013 1
HAG opls_140 -0.013 1
HAH opls_140 -0.013 1
HA4 opls_140 -0.013 1
HA5 opls_140 -0.013 1
HBA opls_140 -0.013 1
HBB opls_140 -0.013 1
HBC opls_140 -0.013 1
HBD opls_140 -0.013 1
HBF opls_140 -0.013 1
HBG opls_140 -0.013 1
HBE opls_140 -0.013 1
 [ bonds ]
 CAY HA1
 CAY HA2
 CAY HA3
 CAX CAY
 CAX HAZ
 CAX HA0
 CAX CAW
 CAW HAX
 CAW HAY
 CAW CAV
 CAV HAV
 CAV HAW
 CAV OAU
 CAS OAU
 CAS OAT
 CAS NAO
 NAO HAO
 CAE NAO
 CAE CAF
 CAE CAD
 CAF HAF
 CAF CAA
 CAA HAA
 CAB CAA
 CAD HAD
 CAD CAC
 CAC HAC
 CAB CAC
 CAB CAG
 CAG HAG
 CAG HAH
 CAH CAG
 CAH CAM
 CAH CAI
 CAM HAM
 CAM CAL
 CAL HAL
 CAK CAL
 CAI HAI
 CAI CAJ
 CAJ HAJ
 CAK CAJ
 CAK NAN
 NAN HAN
 CAP NAN
 CAP OAQ
 CAP OAR
 CAZ OAR
 CAZ HA4
 CAZ HA5
 CAZ CBA
 CBA HBA
 CBA HBB
 CBA CBB
 CBB HBC
 CBB HBD
 CBB CBC
 CBC HBF
 CBC HBG
 CBC HBE

ffbonded.itp file modified with the relevant bonds as below (part has
mentioned below)

CAY   HA1 10.10900   284512.0   ;
  CAY   HA2 10.10900   284512.0   ;
  CAY   HA3 10.10900   284512.0   ;
  CAX   CAY 10.15220   265265.6   ;
  CAX   HAZ 10.10900   284512.0   ;



As I said before, you cannot use atom names in ffbonded.itp.


I know atom name is irrelevant but im bit confused how to write .rtp


without names for my 59

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,
>>
>> 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 ?  If so how i
>> should modify ffnonbonded.itp (I have attached my .rtp file herewith)
>>
>>
> You do not need to modify ffnonbonded.itp.
>
> You added an atom name in ffbonded.itp - this makes no sense and you
> cannot do it.  Bonded and nonbonded interactions are defined by type.
>
> You must use atom names only in .rtp files, because the .rtp entry tells
> pdb2gmx which atoms are bonded, and how.  You can't do that by type because
> that is not a unique way to identify connectivity.  The list of [bonds] in
> the .rtp just tells pdb2gmx which atoms are connect, it is separate from a
> [bondtypes] directive, which says what parameters are assigned to each
> interaction type.
>
> -Justin
>
>
>
>> Regards
>> Sameera
>>
>> On Sun, Sep 18, 2016 at 10:45 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> 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.  You can't force them into
>>> working with OPLS-AA.  It's fundamentally wrong.
>>>
>>> If you want free help with a problem, you have to provide full
>>> information. Fragments of .rtp files are not helpful and it's a waste of
>>> time for those who are trying to give you advice.
>>>
>>>
>>> [ bondedtypes ]
>>>
 ; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14
 RemoveDih
   1  1   3  1

 ; MDI
 [ MD ]
  [ atoms ]
 CAY opls_135 0 1
 CAX opls_135 0.048 2
 CAW opls_135 0.047 2
 CAV opls_135 0.144 2
 OAU opls_154 -0.112 2
 CAS opls_131 0.219 2
 OAT opls_236 -0.41 2
 NAO opls_900 0.073 2
 HAO opls_250 -0.009 2
 CAE opls_260 0.056 3
 CAF opls_145 -0.018 3
 HAF opls_140 0.004 3
 CAA opls_145 -0.018 3
 HAA opls_140 0.004 3
 CAD opls_145 -0.018 3
 HAD opls_140 0.004 3
 CAC opls_145 -0.018 3
 HAC opls_140 0.004 3
 CAB opls_145 -0.022 4
 CAG opls_071 0.044 4
 CAH opls_145 -0.022 4
 CAM opls_145 -0.008 5
 HAM opls_140 0.008 5
 CAL opls_145 -0.008 6
 HAL opls_140 0.008 6
 CAI opls_145 -0.008 7
 HAI opls_140 0.008 7
 CAJ opls_145 -0.008 8
 HAJ opls_140 0.008 8
 CAK opls_145 0.072 9
 NAN opls_900 0.072 9
 HAN opls_250 -0.009 9
 CAP opls_131 0.214 9
 OAQ opls_236 -0.419 9
 OAR opls_154 -0.115 9
 CAZ opls_135 0.14 9
 CBA opls_135 0.045 9
 CBB opls_135 0.01 10
 CBC opls_135 -0.01 10
 HA1 opls_140 -0.013 1
 HA2 opls_140 -0.013 1
 HA3 opls_140 -0.014 1
 HAZ opls_140 -0.013 1
 HA0 opls_140 -0.013 1
 HAX opls_140 -0.013 1
 HAY opls_140 -0.013 1
 HAV opls_140 -0.013 1
 HAW opls_140 -0.013 1
 HAG opls_140 -0.013 1
 HAH opls_140 -0.013 1
 HA4 opls_140 -0.013 1
 HA5 opls_140 -0.013 1
 HBA opls_140 -0.013 1
 HBB opls_140 -0.013 1
 HBC opls_140 -0.013 1
 HBD opls_140 -0.013 1
 HBF opls_140 -0.013 1
 HBG opls_140 -0.013 1
 HBE opls_140 -0.013 1
  [ bonds ]
  CAY HA1
  CAY HA2
  CAY HA3
  CAX CAY
  CAX HAZ
  CAX HA0
  CAX CAW
  CAW HAX
  CAW HAY
  CAW CAV
  CAV HAV
  CAV HAW
  CAV OAU
  CAS OAU
  CAS OAT
  CAS NAO
  NAO HAO
  CAE NAO
  CAE CAF
  CAE CAD
  CAF HAF
  CAF CAA
  CAA HAA
  CAB CAA
  CAD HAD
  CAD CAC
  CAC HAC
  CAB CAC
  CAB CAG
  CAG HAG
  CAG HAH
  CAH CAG
  CAH CAM
  CAH CAI
  CAM HAM
  CAM CAL
  CAL HAL
  CAK CAL
  CAI HAI
  CAI CAJ
  CAJ HAJ
  CAK CAJ
  CAK NAN
  NAN HAN
  CAP NAN
  CAP OAQ
  CAP OAR
  CAZ OAR
  CAZ HA4
  CAZ HA5
  CAZ CBA
  CBA HBA
  CBA HBB
  CBA CBB
  CBB HBC
  CBB HBD
  CBB CBC
  CBC HBF
  CBC HBG
  CBC HBE

 ffbonded.itp file modified with the relevant bonds as below (part has
 mentioned below)

 CAY

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
bond_atomtype' error  which occurring while runing grompp ?  If so how i
should modify ffnonbonded.itp (I have attached my .rtp file herewith)



You do not need to modify ffnonbonded.itp.

You added an atom name in ffbonded.itp - this makes no sense and you cannot do 
it.  Bonded and nonbonded interactions are defined by type.


You must use atom names only in .rtp files, because the .rtp entry tells pdb2gmx 
which atoms are bonded, and how.  You can't do that by type because that is not 
a unique way to identify connectivity.  The list of [bonds] in the .rtp just 
tells pdb2gmx which atoms are connect, it is separate from a [bondtypes] 
directive, which says what parameters are assigned to each interaction type.


-Justin



Regards
Sameera

On Sun, Sep 18, 2016 at 10:45 PM, Justin Lemkul  wrote:




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.  You can't force them into
working with OPLS-AA.  It's fundamentally wrong.

If you want free help with a problem, you have to provide full
information. Fragments of .rtp files are not helpful and it's a waste of
time for those who are trying to give you advice.


[ bondedtypes ]

; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
  1  1   3  1

; MDI
[ MD ]
 [ atoms ]
CAY opls_135 0 1
CAX opls_135 0.048 2
CAW opls_135 0.047 2
CAV opls_135 0.144 2
OAU opls_154 -0.112 2
CAS opls_131 0.219 2
OAT opls_236 -0.41 2
NAO opls_900 0.073 2
HAO opls_250 -0.009 2
CAE opls_260 0.056 3
CAF opls_145 -0.018 3
HAF opls_140 0.004 3
CAA opls_145 -0.018 3
HAA opls_140 0.004 3
CAD opls_145 -0.018 3
HAD opls_140 0.004 3
CAC opls_145 -0.018 3
HAC opls_140 0.004 3
CAB opls_145 -0.022 4
CAG opls_071 0.044 4
CAH opls_145 -0.022 4
CAM opls_145 -0.008 5
HAM opls_140 0.008 5
CAL opls_145 -0.008 6
HAL opls_140 0.008 6
CAI opls_145 -0.008 7
HAI opls_140 0.008 7
CAJ opls_145 -0.008 8
HAJ opls_140 0.008 8
CAK opls_145 0.072 9
NAN opls_900 0.072 9
HAN opls_250 -0.009 9
CAP opls_131 0.214 9
OAQ opls_236 -0.419 9
OAR opls_154 -0.115 9
CAZ opls_135 0.14 9
CBA opls_135 0.045 9
CBB opls_135 0.01 10
CBC opls_135 -0.01 10
HA1 opls_140 -0.013 1
HA2 opls_140 -0.013 1
HA3 opls_140 -0.014 1
HAZ opls_140 -0.013 1
HA0 opls_140 -0.013 1
HAX opls_140 -0.013 1
HAY opls_140 -0.013 1
HAV opls_140 -0.013 1
HAW opls_140 -0.013 1
HAG opls_140 -0.013 1
HAH opls_140 -0.013 1
HA4 opls_140 -0.013 1
HA5 opls_140 -0.013 1
HBA opls_140 -0.013 1
HBB opls_140 -0.013 1
HBC opls_140 -0.013 1
HBD opls_140 -0.013 1
HBF opls_140 -0.013 1
HBG opls_140 -0.013 1
HBE opls_140 -0.013 1
 [ bonds ]
 CAY HA1
 CAY HA2
 CAY HA3
 CAX CAY
 CAX HAZ
 CAX HA0
 CAX CAW
 CAW HAX
 CAW HAY
 CAW CAV
 CAV HAV
 CAV HAW
 CAV OAU
 CAS OAU
 CAS OAT
 CAS NAO
 NAO HAO
 CAE NAO
 CAE CAF
 CAE CAD
 CAF HAF
 CAF CAA
 CAA HAA
 CAB CAA
 CAD HAD
 CAD CAC
 CAC HAC
 CAB CAC
 CAB CAG
 CAG HAG
 CAG HAH
 CAH CAG
 CAH CAM
 CAH CAI
 CAM HAM
 CAM CAL
 CAL HAL
 CAK CAL
 CAI HAI
 CAI CAJ
 CAJ HAJ
 CAK CAJ
 CAK NAN
 NAN HAN
 CAP NAN
 CAP OAQ
 CAP OAR
 CAZ OAR
 CAZ HA4
 CAZ HA5
 CAZ CBA
 CBA HBA
 CBA HBB
 CBA CBB
 CBB HBC
 CBB HBD
 CBB CBC
 CBC HBF
 CBC HBG
 CBC HBE

ffbonded.itp file modified with the relevant bonds as below (part has
mentioned below)

CAY   HA1 10.10900   284512.0   ;
  CAY   HA2 10.10900   284512.0   ;
  CAY   HA3 10.10900   284512.0   ;
  CAX   CAY 10.15220   265265.6   ;
  CAX   HAZ 10.10900   284512.0   ;




As I said before, you cannot use atom names in ffbonded.itp.

I know atom name is irrelevant but im bit confused how to write .rtp

without names for my 59 atom molecule.



The .rtp file *does* use atom names.  See the manual.  That part is fine.
What you cannot do is try to assign parameters using names.  Those require
types.

-Justin




regards

On Sun, Sep 18, 2016 at 10:09 PM, Justin Lemkul  wrote:




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
 atomtype.atp file. But still above error occurring while running
grompp.
Not

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 ?  If so how i
should modify ffnonbonded.itp (I have attached my .rtp file herewith)


Regards
Sameera

On Sun, Sep 18, 2016 at 10:45 PM, Justin Lemkul  wrote:

>
>
> 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.  You can't force them into
> working with OPLS-AA.  It's fundamentally wrong.
>
> If you want free help with a problem, you have to provide full
> information. Fragments of .rtp files are not helpful and it's a waste of
> time for those who are trying to give you advice.
>
>
> [ bondedtypes ]
>> ; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
>>   1  1   3  1
>>
>> ; MDI
>> [ MD ]
>>  [ atoms ]
>> CAY opls_135 0 1
>> CAX opls_135 0.048 2
>> CAW opls_135 0.047 2
>> CAV opls_135 0.144 2
>> OAU opls_154 -0.112 2
>> CAS opls_131 0.219 2
>> OAT opls_236 -0.41 2
>> NAO opls_900 0.073 2
>> HAO opls_250 -0.009 2
>> CAE opls_260 0.056 3
>> CAF opls_145 -0.018 3
>> HAF opls_140 0.004 3
>> CAA opls_145 -0.018 3
>> HAA opls_140 0.004 3
>> CAD opls_145 -0.018 3
>> HAD opls_140 0.004 3
>> CAC opls_145 -0.018 3
>> HAC opls_140 0.004 3
>> CAB opls_145 -0.022 4
>> CAG opls_071 0.044 4
>> CAH opls_145 -0.022 4
>> CAM opls_145 -0.008 5
>> HAM opls_140 0.008 5
>> CAL opls_145 -0.008 6
>> HAL opls_140 0.008 6
>> CAI opls_145 -0.008 7
>> HAI opls_140 0.008 7
>> CAJ opls_145 -0.008 8
>> HAJ opls_140 0.008 8
>> CAK opls_145 0.072 9
>> NAN opls_900 0.072 9
>> HAN opls_250 -0.009 9
>> CAP opls_131 0.214 9
>> OAQ opls_236 -0.419 9
>> OAR opls_154 -0.115 9
>> CAZ opls_135 0.14 9
>> CBA opls_135 0.045 9
>> CBB opls_135 0.01 10
>> CBC opls_135 -0.01 10
>> HA1 opls_140 -0.013 1
>> HA2 opls_140 -0.013 1
>> HA3 opls_140 -0.014 1
>> HAZ opls_140 -0.013 1
>> HA0 opls_140 -0.013 1
>> HAX opls_140 -0.013 1
>> HAY opls_140 -0.013 1
>> HAV opls_140 -0.013 1
>> HAW opls_140 -0.013 1
>> HAG opls_140 -0.013 1
>> HAH opls_140 -0.013 1
>> HA4 opls_140 -0.013 1
>> HA5 opls_140 -0.013 1
>> HBA opls_140 -0.013 1
>> HBB opls_140 -0.013 1
>> HBC opls_140 -0.013 1
>> HBD opls_140 -0.013 1
>> HBF opls_140 -0.013 1
>> HBG opls_140 -0.013 1
>> HBE opls_140 -0.013 1
>>  [ bonds ]
>>  CAY HA1
>>  CAY HA2
>>  CAY HA3
>>  CAX CAY
>>  CAX HAZ
>>  CAX HA0
>>  CAX CAW
>>  CAW HAX
>>  CAW HAY
>>  CAW CAV
>>  CAV HAV
>>  CAV HAW
>>  CAV OAU
>>  CAS OAU
>>  CAS OAT
>>  CAS NAO
>>  NAO HAO
>>  CAE NAO
>>  CAE CAF
>>  CAE CAD
>>  CAF HAF
>>  CAF CAA
>>  CAA HAA
>>  CAB CAA
>>  CAD HAD
>>  CAD CAC
>>  CAC HAC
>>  CAB CAC
>>  CAB CAG
>>  CAG HAG
>>  CAG HAH
>>  CAH CAG
>>  CAH CAM
>>  CAH CAI
>>  CAM HAM
>>  CAM CAL
>>  CAL HAL
>>  CAK CAL
>>  CAI HAI
>>  CAI CAJ
>>  CAJ HAJ
>>  CAK CAJ
>>  CAK NAN
>>  NAN HAN
>>  CAP NAN
>>  CAP OAQ
>>  CAP OAR
>>  CAZ OAR
>>  CAZ HA4
>>  CAZ HA5
>>  CAZ CBA
>>  CBA HBA
>>  CBA HBB
>>  CBA CBB
>>  CBB HBC
>>  CBB HBD
>>  CBB CBC
>>  CBC HBF
>>  CBC HBG
>>  CBC HBE
>>
>> ffbonded.itp file modified with the relevant bonds as below (part has
>> mentioned below)
>>
>> CAY   HA1 10.10900   284512.0   ;
>>   CAY   HA2 10.10900   284512.0   ;
>>   CAY   HA3 10.10900   284512.0   ;
>>   CAX   CAY 10.15220   265265.6   ;
>>   CAX   HAZ 10.10900   284512.0   ;
>>
>>
>>
> As I said before, you cannot use atom names in ffbonded.itp.
>
> I know atom name is irrelevant but im bit confused how to write .rtp
>> without names for my 59 atom molecule.
>>
>>
> The .rtp file *does* use atom names.  See the manual.  That part is fine.
> What you cannot do is try to assign parameters using names.  Those require
> types.
>
> -Justin
>
>
>
>> regards
>>
>> On Sun, Sep 18, 2016 at 10:09 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> 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
  atomtype.atp file. But still above error occurring while running
 grompp.
 Not sure should i add again thes atoms to atp file and if so how to add
 them. Part of my rtp file is as below,

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.  You can't force them into working with 
OPLS-AA.  It's fundamentally wrong.


If you want free help with a problem, you have to provide full information. 
Fragments of .rtp files are not helpful and it's a waste of time for those who 
are trying to give you advice.



[ bondedtypes ]
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
  1  1   3  1

; MDI
[ MD ]
 [ atoms ]
CAY opls_135 0 1
CAX opls_135 0.048 2
CAW opls_135 0.047 2
CAV opls_135 0.144 2
OAU opls_154 -0.112 2
CAS opls_131 0.219 2
OAT opls_236 -0.41 2
NAO opls_900 0.073 2
HAO opls_250 -0.009 2
CAE opls_260 0.056 3
CAF opls_145 -0.018 3
HAF opls_140 0.004 3
CAA opls_145 -0.018 3
HAA opls_140 0.004 3
CAD opls_145 -0.018 3
HAD opls_140 0.004 3
CAC opls_145 -0.018 3
HAC opls_140 0.004 3
CAB opls_145 -0.022 4
CAG opls_071 0.044 4
CAH opls_145 -0.022 4
CAM opls_145 -0.008 5
HAM opls_140 0.008 5
CAL opls_145 -0.008 6
HAL opls_140 0.008 6
CAI opls_145 -0.008 7
HAI opls_140 0.008 7
CAJ opls_145 -0.008 8
HAJ opls_140 0.008 8
CAK opls_145 0.072 9
NAN opls_900 0.072 9
HAN opls_250 -0.009 9
CAP opls_131 0.214 9
OAQ opls_236 -0.419 9
OAR opls_154 -0.115 9
CAZ opls_135 0.14 9
CBA opls_135 0.045 9
CBB opls_135 0.01 10
CBC opls_135 -0.01 10
HA1 opls_140 -0.013 1
HA2 opls_140 -0.013 1
HA3 opls_140 -0.014 1
HAZ opls_140 -0.013 1
HA0 opls_140 -0.013 1
HAX opls_140 -0.013 1
HAY opls_140 -0.013 1
HAV opls_140 -0.013 1
HAW opls_140 -0.013 1
HAG opls_140 -0.013 1
HAH opls_140 -0.013 1
HA4 opls_140 -0.013 1
HA5 opls_140 -0.013 1
HBA opls_140 -0.013 1
HBB opls_140 -0.013 1
HBC opls_140 -0.013 1
HBD opls_140 -0.013 1
HBF opls_140 -0.013 1
HBG opls_140 -0.013 1
HBE opls_140 -0.013 1
 [ bonds ]
 CAY HA1
 CAY HA2
 CAY HA3
 CAX CAY
 CAX HAZ
 CAX HA0
 CAX CAW
 CAW HAX
 CAW HAY
 CAW CAV
 CAV HAV
 CAV HAW
 CAV OAU
 CAS OAU
 CAS OAT
 CAS NAO
 NAO HAO
 CAE NAO
 CAE CAF
 CAE CAD
 CAF HAF
 CAF CAA
 CAA HAA
 CAB CAA
 CAD HAD
 CAD CAC
 CAC HAC
 CAB CAC
 CAB CAG
 CAG HAG
 CAG HAH
 CAH CAG
 CAH CAM
 CAH CAI
 CAM HAM
 CAM CAL
 CAL HAL
 CAK CAL
 CAI HAI
 CAI CAJ
 CAJ HAJ
 CAK CAJ
 CAK NAN
 NAN HAN
 CAP NAN
 CAP OAQ
 CAP OAR
 CAZ OAR
 CAZ HA4
 CAZ HA5
 CAZ CBA
 CBA HBA
 CBA HBB
 CBA CBB
 CBB HBC
 CBB HBD
 CBB CBC
 CBC HBF
 CBC HBG
 CBC HBE

ffbonded.itp file modified with the relevant bonds as below (part has
mentioned below)

CAY   HA1 10.10900   284512.0   ;
  CAY   HA2 10.10900   284512.0   ;
  CAY   HA3 10.10900   284512.0   ;
  CAX   CAY 10.15220   265265.6   ;
  CAX   HAZ 10.10900   284512.0   ;




As I said before, you cannot use atom names in ffbonded.itp.


I know atom name is irrelevant but im bit confused how to write .rtp
without names for my 59 atom molecule.



The .rtp file *does* use atom names.  See the manual.  That part is fine.  What 
you cannot do is try to assign parameters using names.  Those require types.


-Justin



regards

On Sun, Sep 18, 2016 at 10:09 PM, Justin Lemkul  wrote:




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
 atomtype.atp file. But still above error occurring while running grompp.
Not sure should i add again thes atoms to atp file and if so how to add
them. Part of my rtp file is as below, I have modified the ffbonded.itp
(only bond types added) successfully.



What did you add to ffbonded.itp?  Whatever it was is causing an error.
Based on the .rtp entry below, it looks like you tried to use atom names in
ffbonded.itp.  That's not right.  All interactions (bonded and nonbonded)
are defined by atom type.  The name is irrelevant.  If you're re-using only
OPLS-AA atom types, most of the bonded interactions should be present
already.

[ bondedtypes ]

; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
  1  1   3  1



You're missing entries here if you're trying to create an OPLS-derived
force field.  Look at oplsaa.ff/aminoacids.rtp

; MDI

[ MD ]
 [ atoms ]
CAY opls_135  0.000  1
CAX opls_135  0.048 2
CAW opls_135  0.047 2
CAV opls_135  0.144 2
OAU opls_154 -0.112 2



This can't possibly be right.  You've defined only heavy atoms (OPLS-AA is
an all-atom force field, so there should be H) and the net charge of this
residue is +0.117, which

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
 atomtype.atp file. But still above error occurring while running grompp.
Not sure should i add again thes atoms to atp file and if so how to add
them. Part of my rtp file is as below, I have modified the ffbonded.itp
(only bond types added) successfully.



What did you add to ffbonded.itp?  Whatever it was is causing an error.  Based 
on the .rtp entry below, it looks like you tried to use atom names in 
ffbonded.itp.  That's not right.  All interactions (bonded and nonbonded) are 
defined by atom type.  The name is irrelevant.  If you're re-using only OPLS-AA 
atom types, most of the bonded interactions should be present already.



[ bondedtypes ]
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
  1  1   3  1



You're missing entries here if you're trying to create an OPLS-derived force 
field.  Look at oplsaa.ff/aminoacids.rtp



; MDI
[ MD ]
 [ atoms ]
CAY opls_135  0.000  1
CAX opls_135  0.048 2
CAW opls_135  0.047 2
CAV opls_135  0.144 2
OAU opls_154 -0.112 2



This can't possibly be right.  You've defined only heavy atoms (OPLS-AA is an 
all-atom force field, so there should be H) and the net charge of this residue 
is +0.117, which is physical nonsense.  Based on the names and suspect charges, 
it looks like you're just porting over a PRODRG united-atom topology and trying 
to call it OPLS-AA.  That's not going to work.


Note that you also need [bonds] if you want the residue to actually be 
chemically reasonable, otherwise it's just a collection of atoms sitting near 
one another, which will immediately explode if you try to run a simulation.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[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 while running grompp.
Not sure should i add again thes atoms to atp file and if so how to add
them. Part of my rtp file is as below, I have modified the ffbonded.itp
(only bond types added) successfully.

[ bondedtypes ]
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
  1  1   3  1

; MDI
[ MD ]
 [ atoms ]
CAY opls_135  0.000  1
CAX opls_135  0.048 2
CAW opls_135  0.047 2
CAV opls_135  0.144 2
OAU opls_154 -0.112 2


Your little help is much appreciate for this.
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Re: [gmx-users] Unknown bond_atomtype

2016-02-17 Thread Nash, Anthony

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"
 wrote:

>
>
>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 I¹ve 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 with very little changes to the topol file after running
>> pdb2gmx. I do have a couple of questions that I hope you could help me
>> with.
>>
>> 1) For grompp to compile successfully, must every molecule/residue have
>>a
>> complete set of dihedral angle force constants?
>
>grompp will complain about any missing parameters, triggering a failure.
>
>> 2) It appears as though the residue to residue bond connectivity in my
>> force field files aren¹t correctly parameterised. In NGLY-MOD-CGLY, a
>> bonded term is added to the topol for the C in NGLY to the N in CGLY. To
>> avoid this must I add an entry such as -C N in the [ bonds ] section of
>> the [ MOD1 ] residue definition in aminoacids.rtp? I¹m unsure what ³-C²
>> means.
>>
>
>- indicates an atom in the previous residue, + means in the next residue.
> So -C 
>is the C in the previous residue.  If you're getting bonds between NGLY
>and 
>CGLY, ignoring the intervening residue, you probably either haven't set
>your 
>modified residue as Protein in residuetypes.dat or it doesn't have a C
>(which it 
>should, if it's an amino acid.
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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Re: [gmx-users] Unknown bond_atomtype

2016-02-17 Thread Justin Lemkul




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 correct so an MD simulation can be
generated with very little changes to the topol file after running
pdb2gmx. I do have a couple of questions that I hope you could help me
with.

1) For grompp to compile successfully, must every molecule/residue have a
complete set of dihedral angle force constants?


grompp will complain about any missing parameters, triggering a failure.


2) It appears as though the residue to residue bond connectivity in my
force field files aren’t correctly parameterised. In NGLY-MOD-CGLY, a
bonded term is added to the topol for the C in NGLY to the N in CGLY. To
avoid this must I add an entry such as -C N in the [ bonds ] section of
the [ MOD1 ] residue definition in aminoacids.rtp? I’m unsure what “-C”
means.



- indicates an atom in the previous residue, + means in the next residue.  So -C 
is the C in the previous residue.  If you're getting bonds between NGLY and 
CGLY, ignoring the intervening residue, you probably either haven't set your 
modified residue as Protein in residuetypes.dat or it doesn't have a C (which it 
should, if it's an amino acid.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Unknown bond_atomtype

2016-02-17 Thread Nash, Anthony

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 with very little changes to the topol file after running
pdb2gmx. I do have a couple of questions that I hope you could help me
with. 

1) For grompp to compile successfully, must every molecule/residue have a
complete set of dihedral angle force constants?
2) It appears as though the residue to residue bond connectivity in my
force field files aren’t correctly parameterised. In NGLY-MOD-CGLY, a
bonded term is added to the topol for the C in NGLY to the N in CGLY. To
avoid this must I add an entry such as -C N in the [ bonds ] section of
the [ MOD1 ] residue definition in aminoacids.rtp? I’m unsure what “-C”
means.

Thanks for all your help.

Anthony


Dr Anthony Nash
Department of Chemistry
University College London





On 17/02/2016 21:46, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"  wrote:

>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
>parameters need to go into the databases for grompp to look up (or then
>can
>also go in the [bonds] section of the .rtp, I think).
>
>Mark
>
>On Wed, Feb 17, 2016 at 10:39 PM Nash, Anthony  wrote:
>
>>
>> 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"
>> > a.n...@ucl.ac.uk> wrote:
>>
>> >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. Every non-terminal amino acid has a
>>-C
>> >N line in [ bonds ]. My custom residue does not. I assume this is to do
>> >with amino acid connectivity. How do I implement this single bond if I
>> >have the connectivity NGLY-MOD-CGLY, where EVERY atom in MOD is
>>completely
>> >new? I assume this is where you meant use existing types. So in theory
>>I
>> >could just change the very first atom of MOD, which would be MN1 to N,
>>and
>> >then go into ffbonded and just change MN1-MC1 to N-MC1 for the first
>>bond
>> >parameter the MOD residue.
>> >
>> >Apologies for rambling on, I *think* I know what I am doing.
>> >
>> >Thanks
>> >Anthony
>> >
>> >Dr Anthony Nash
>> >Department of Chemistry
>> >University College London
>> >
>> >
>> >
>> >
>> >
>> >On 17/02/2016 17:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>> on
>> >behalf of Nash, Anthony"
>> >> >a.n...@ucl.ac.uk> wrote:
>> >
>> >>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
>>within
>> >>the [atom] section of my new residue?
>> >>
>> >>Also, I am guessing there is no issue with atom NAME and TYPE being
>> >>identical?
>> >>
>> >>Many thanks
>> >>Anthony
>> >>
>> >>Dr Anthony Nash
>> >>Department of Chemistry
>> >>University College London
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>On 17/02/2016 16:43,
>>"gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>> >>on
>> >>behalf of Mark Abraham"
>> >>> >>on behalf of mark.j.abra...@gmail.com> wrote:
>> >>
>> >>>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 (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
>>  problems.
>> 
>>  Unfortunately when I run

Re: [gmx-users] Unknown bond_atomtype

2016-02-17 Thread Mark Abraham

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
parameters need to go into the databases for grompp to look up (or then can
also go in the [bonds] section of the .rtp, I think).

Mark

On Wed, Feb 17, 2016 at 10:39 PM Nash, Anthony  wrote:

>
> 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"
>  a.n...@ucl.ac.uk> wrote:
>
> >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. Every non-terminal amino acid has a -C
> >N line in [ bonds ]. My custom residue does not. I assume this is to do
> >with amino acid connectivity. How do I implement this single bond if I
> >have the connectivity NGLY-MOD-CGLY, where EVERY atom in MOD is completely
> >new? I assume this is where you meant use existing types. So in theory I
> >could just change the very first atom of MOD, which would be MN1 to N, and
> >then go into ffbonded and just change MN1-MC1 to N-MC1 for the first bond
> >parameter the MOD residue.
> >
> >Apologies for rambling on, I *think* I know what I am doing.
> >
> >Thanks
> >Anthony
> >
> >Dr Anthony Nash
> >Department of Chemistry
> >University College London
> >
> >
> >
> >
> >
> >On 17/02/2016 17:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> on
> >behalf of Nash, Anthony"
> > >a.n...@ucl.ac.uk> wrote:
> >
> >>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 within
> >>the [atom] section of my new residue?
> >>
> >>Also, I am guessing there is no issue with atom NAME and TYPE being
> >>identical?
> >>
> >>Many thanks
> >>Anthony
> >>
> >>Dr Anthony Nash
> >>Department of Chemistry
> >>University College London
> >>
> >>
> >>
> >>
> >>
> >>On 17/02/2016 16:43, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> >>on
> >>behalf of Mark Abraham"
> >> >>on behalf of mark.j.abra...@gmail.com> wrote:
> >>
> >>>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 (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
>  problems.
> 
>  Unfortunately when I run grompp (5.0.4) I get the following error:
> 
>  Fatal error:
>  Unknown bond_atomtype MN1 <‹‹ first atom in my new residue
> 
> 
>  At first I thought my topology might be pointing to the wrong
> forcefield,
>  but I¹ve checked and double checked:
> 
>  #include
> "/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
>  #include "modic.itp"
>  ;#ifdef POSRES
>  ;#include "posre.itp"
>  ;#endif
> 
>  [ system ]
>  ; Name
>  MODIC with glycine terminal ends
> 
>  [ molecules ]
>  ; Compound#mols
>  MODIC 1
> 
> 
>  I¹m going to take a guess at what the problem is. Each of the atoms in
> the
>  residue was derived from scratch.Therefore, they have a completely new
>  type. I wasn¹t feeling very creative with my naming convention so the
> atom
>  name and the atom type are identical e.g.,
> 
>  ;MODIC crosslink
>  [ MOD1 ]
>   [ atoms ]
>  ; NAMETYPECHARGE  NUMBER
>  MN1 MN1 -0.3640 1
>  MC1 MC1 0.0358  2
>  MC15MC150.4871  3
>  Š
> 
>  Š
> 
>  Will this have confused grompp?
> 
>  Many thanks
>  Anthony
> 
>  Dr Anthony Nash
>  Department of Chemistry
>

Re: [gmx-users] Unknown bond_atomtype

2016-02-17 Thread Nash, Anthony


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"
 wrote:

>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. Every non-terminal amino acid has a -C
>N line in [ bonds ]. My custom residue does not. I assume this is to do
>with amino acid connectivity. How do I implement this single bond if I
>have the connectivity NGLY-MOD-CGLY, where EVERY atom in MOD is completely
>new? I assume this is where you meant use existing types. So in theory I
>could just change the very first atom of MOD, which would be MN1 to N, and
>then go into ffbonded and just change MN1-MC1 to N-MC1 for the first bond
>parameter the MOD residue.
>
>Apologies for rambling on, I *think* I know what I am doing.
>
>Thanks
>Anthony
>
>Dr Anthony Nash
>Department of Chemistry
>University College London
>
>
>
>
>
>On 17/02/2016 17:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
>behalf of Nash, Anthony"
>a.n...@ucl.ac.uk> wrote:
>
>>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 within
>>the [atom] section of my new residue?
>>
>>Also, I am guessing there is no issue with atom NAME and TYPE being
>>identical?
>>
>>Many thanks
>>Anthony
>>
>>Dr Anthony Nash
>>Department of Chemistry
>>University College London
>>
>>
>>
>>
>>
>>On 17/02/2016 16:43, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>on
>>behalf of Mark Abraham"
>>>on behalf of mark.j.abra...@gmail.com> wrote:
>>
>>>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 (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
 problems.

 Unfortunately when I run grompp (5.0.4) I get the following error:

 Fatal error:
 Unknown bond_atomtype MN1 <‹‹ first atom in my new residue


 At first I thought my topology might be pointing to the wrong
forcefield,
 but I¹ve checked and double checked:

 #include 
"/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
 #include "modic.itp"
 ;#ifdef POSRES
 ;#include "posre.itp"
 ;#endif

 [ system ]
 ; Name
 MODIC with glycine terminal ends

 [ molecules ]
 ; Compound#mols
 MODIC 1


 I¹m going to take a guess at what the problem is. Each of the atoms in
the
 residue was derived from scratch.Therefore, they have a completely new
 type. I wasn¹t feeling very creative with my naming convention so the
atom
 name and the atom type are identical e.g.,

 ;MODIC crosslink
 [ MOD1 ]
  [ atoms ]
 ; NAMETYPECHARGE  NUMBER
 MN1 MN1 -0.3640 1
 MC1 MC1 0.0358  2
 MC15MC150.4871  3
 Š

 Š

 Will this have confused grompp?

 Many thanks
 Anthony

 Dr Anthony Nash
 Department of Chemistry
 University College London



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

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 * For (un)subscribe requests visit
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Re: [gmx-users] Unknown bond_atomtype

2016-02-17 Thread Nash, Anthony

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. Every non-terminal amino acid has a -C
N line in [ bonds ]. My custom residue does not. I assume this is to do
with amino acid connectivity. How do I implement this single bond if I
have the connectivity NGLY-MOD-CGLY, where EVERY atom in MOD is completely
new? I assume this is where you meant use existing types. So in theory I
could just change the very first atom of MOD, which would be MN1 to N, and
then go into ffbonded and just change MN1-MC1 to N-MC1 for the first bond
parameter the MOD residue.

Apologies for rambling on, I *think* I know what I am doing.

Thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London





On 17/02/2016 17:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Nash, Anthony"
 wrote:

>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 within
>the [atom] section of my new residue?
>
>Also, I am guessing there is no issue with atom NAME and TYPE being
>identical?
>
>Many thanks
>Anthony
>
>Dr Anthony Nash
>Department of Chemistry
>University College London
>
>
>
>
>
>On 17/02/2016 16:43, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
>behalf of Mark Abraham" on behalf of mark.j.abra...@gmail.com> wrote:
>
>>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 (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
>>> problems.
>>>
>>> Unfortunately when I run grompp (5.0.4) I get the following error:
>>>
>>> Fatal error:
>>> Unknown bond_atomtype MN1 <‹‹ first atom in my new residue
>>>
>>>
>>> At first I thought my topology might be pointing to the wrong
>>>forcefield,
>>> but I¹ve checked and double checked:
>>>
>>> #include 
>>>"/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
>>> #include "modic.itp"
>>> ;#ifdef POSRES
>>> ;#include "posre.itp"
>>> ;#endif
>>>
>>> [ system ]
>>> ; Name
>>> MODIC with glycine terminal ends
>>>
>>> [ molecules ]
>>> ; Compound#mols
>>> MODIC 1
>>>
>>>
>>> I¹m going to take a guess at what the problem is. Each of the atoms in
>>>the
>>> residue was derived from scratch.Therefore, they have a completely new
>>> type. I wasn¹t feeling very creative with my naming convention so the
>>>atom
>>> name and the atom type are identical e.g.,
>>>
>>> ;MODIC crosslink
>>> [ MOD1 ]
>>>  [ atoms ]
>>> ; NAMETYPECHARGE  NUMBER
>>> MN1 MN1 -0.3640 1
>>> MC1 MC1 0.0358  2
>>> MC15MC150.4871  3
>>> Š
>>>
>>> Š
>>>
>>> Will this have confused grompp?
>>>
>>> Many thanks
>>> Anthony
>>>
>>> Dr Anthony Nash
>>> Department of Chemistry
>>> University College London
>>>
>>>
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>-- 
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>>
>>* Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>posting!
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>>
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>>send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Unknown bond_atomtype

2016-02-17 Thread Nash, Anthony

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 within
the [atom] section of my new residue?

Also, I am guessing there is no issue with atom NAME and TYPE being
identical?

Many thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London





On 17/02/2016 16:43, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"  wrote:

>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 (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
>> problems.
>>
>> Unfortunately when I run grompp (5.0.4) I get the following error:
>>
>> Fatal error:
>> Unknown bond_atomtype MN1 <‹‹ first atom in my new residue
>>
>>
>> At first I thought my topology might be pointing to the wrong
>>forcefield,
>> but I¹ve checked and double checked:
>>
>> #include 
>>"/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
>> #include "modic.itp"
>> ;#ifdef POSRES
>> ;#include "posre.itp"
>> ;#endif
>>
>> [ system ]
>> ; Name
>> MODIC with glycine terminal ends
>>
>> [ molecules ]
>> ; Compound#mols
>> MODIC 1
>>
>>
>> I¹m going to take a guess at what the problem is. Each of the atoms in
>>the
>> residue was derived from scratch.Therefore, they have a completely new
>> type. I wasn¹t feeling very creative with my naming convention so the
>>atom
>> name and the atom type are identical e.g.,
>>
>> ;MODIC crosslink
>> [ MOD1 ]
>>  [ atoms ]
>> ; NAMETYPECHARGE  NUMBER
>> MN1 MN1 -0.3640 1
>> MC1 MC1 0.0358  2
>> MC15MC150.4871  3
>> Š
>>
>> Š
>>
>> Will this have confused grompp?
>>
>> Many thanks
>> Anthony
>>
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>>
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>-- 
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>
>* Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>send a mail to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] Unknown bond_atomtype

2016-02-17 Thread Mark Abraham

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 (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
> problems.
>
> Unfortunately when I run grompp (5.0.4) I get the following error:
>
> Fatal error:
> Unknown bond_atomtype MN1 <‹‹ first atom in my new residue
>
>
> At first I thought my topology might be pointing to the wrong forcefield,
> but I¹ve checked and double checked:
>
> #include "/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
> #include "modic.itp"
> ;#ifdef POSRES
> ;#include "posre.itp"
> ;#endif
>
> [ system ]
> ; Name
> MODIC with glycine terminal ends
>
> [ molecules ]
> ; Compound#mols
> MODIC 1
>
>
> I¹m going to take a guess at what the problem is. Each of the atoms in the
> residue was derived from scratch.Therefore, they have a completely new
> type. I wasn¹t feeling very creative with my naming convention so the atom
> name and the atom type are identical e.g.,
>
> ;MODIC crosslink
> [ MOD1 ]
>  [ atoms ]
> ; NAMETYPECHARGE  NUMBER
> MN1 MN1 -0.3640 1
> MC1 MC1 0.0358  2
> MC15MC150.4871  3
> Š
>
> Š
>
> Will this have confused grompp?
>
> Many thanks
> Anthony
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
>
>
>
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> Gromacs Users mailing list
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[gmx-users] Unknown bond_atomtype

2016-02-17 Thread Nash, Anthony

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
problems.  

Unfortunately when I run grompp (5.0.4) I get the following error:

Fatal error:
Unknown bond_atomtype MN1 <‹‹ first atom in my new residue


At first I thought my topology might be pointing to the wrong forcefield,
but I¹ve checked and double checked:

#include "/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
#include "modic.itp"
;#ifdef POSRES
;#include "posre.itp"
;#endif

[ system ]
; Name
MODIC with glycine terminal ends

[ molecules ]
; Compound#mols
MODIC 1


I¹m going to take a guess at what the problem is. Each of the atoms in the
residue was derived from scratch.Therefore, they have a completely new
type. I wasn¹t feeling very creative with my naming convention so the atom
name and the atom type are identical e.g.,

;MODIC crosslink
[ MOD1 ]
 [ atoms ]
; NAMETYPECHARGE  NUMBER
MN1 MN1 -0.3640 1
MC1 MC1 0.0358  2
MC15MC150.4871  3
Š

Š

Will this have confused grompp?

Many thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London



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

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Re: [gmx-users] Unknown bond_atomtype CAY

Re: [gmx-users] Unknown bond_atomtype CAY

Re: [gmx-users] Unknown bond_atomtype CAY

Re: [gmx-users] Unknown bond_atomtype CAY

Re: [gmx-users] Unknown bond_atomtype CAY

Re: [gmx-users] Unknown bond_atomtype CAY

Re: [gmx-users] Unknown bond_atomtype CAY

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[gmx-users] Unknown bond_atomtype CAY

Re: [gmx-users] Unknown bond_atomtype

Re: [gmx-users] Unknown bond_atomtype

Re: [gmx-users] Unknown bond_atomtype

Re: [gmx-users] Unknown bond_atomtype

Re: [gmx-users] Unknown bond_atomtype

Re: [gmx-users] Unknown bond_atomtype

Re: [gmx-users] Unknown bond_atomtype

Re: [gmx-users] Unknown bond_atomtype

[gmx-users] Unknown bond_atomtype

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