Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

Justin A. Lemkul Tue, 27 Mar 2012 16:21:55 -0700


bipin singh wrote:

Thanks for your suggestions.

Now I am getting the following error during grompp

Warning: atom name 1 in topol.top and box_prot_oct_sol.gro does not
match (C1 - N)
Warning: atom name 5 in topol.top and box_prot_oct_sol.gro does not
match (C2 - CA)
Warning: atom name 6 in topol.top and box_prot_oct_sol.gro does not
match (H4 - HA)
Warning: atom name 7 in topol.top and box_prot_oct_sol.gro does not
match (H5 - CB)
Warning: atom name 8 in topol.top and box_prot_oct_sol.gro does not
match (C3 - HB1)
Warning: atom name 9 in topol.top and box_prot_oct_sol.gro does not
match (H6 - HB2)
Warning: atom name 10 in topol.top and box_prot_oct_sol.gro does not
match (H7 - OG)
Warning: atom name 11 in topol.top and box_prot_oct_sol.gro does not
match (C4 - HG)
Warning: atom name 12 in topol.top and box_prot_oct_sol.gro does not
match (H8 - C)
Warning: atom name 13 in topol.top and box_prot_oct_sol.gro does not
match (H9 - O)
Warning: atom name 14 in topol.top and box_prot_oct_sol.gro does not
match (C5 - N)
Warning: atom name 15 in topol.top and box_prot_oct_sol.gro does not
match (H10 - H)
Warning: atom name 16 in topol.top and box_prot_oct_sol.gro does not
match (H11 - CA)
Warning: atom name 17 in topol.top and box_prot_oct_sol.gro does not
match (C6 - HA)
Warning: atom name 18 in topol.top and box_prot_oct_sol.gro does not
match (H12 - CB)
Warning: atom name 19 in topol.top and box_prot_oct_sol.gro does not
match (H13 - HB1)
Warning: atom name 20 in topol.top and box_prot_oct_sol.gro does not
match (C7 - HB2)
Warning: atom name 21 in topol.top and box_prot_oct_sol.gro does not
match (H14 - CG)
Warning: atom name 22 in topol.top and box_prot_oct_sol.gro does not
match (H15 - HG)
Warning: atom name 23 in topol.top and box_prot_oct_sol.gro does not
match (C8 - CD1)
(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 55]:
  28782 non-matching atom names
  atom names from topol.top will be used
  atom names from box_prot_oct_sol.gro will be ignored

The order of atoms in coordinate file and order of [molecules]
directive are same.

If that were true, you wouldn't be getting this error. Check your files verycarefully. Something doesn't line up.


-Justin

I have checked on the gromacs forum and also the documentation but not
able to rectify the problem.



This is how I included the octane topology in .top file
#########################################
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"
#include "oct.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Ion_chain_A2.itp"

; Include water topology
#include "amber99sb-ildn.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "amber99sb-ildn.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Ion_chain_A2        1
SOL               565
1-octanol         1
SOL              8422
####################################

Please provide suggestions.

On Tue, Mar 27, 2012 at 17:59, Justin A. Lemkul <[email protected]> wrote:


bipin singh wrote:

Thanks for your inputs.
I have followed your suggestion and included the .itp for the octane
molecule (containing atomtype definition for new atoms) in the
topology file(.top) of the whole system (prot+oct+water). but during
grompp it produce error and results in termination due to non matching
numbers (27 atoms of octane molecule) between coordinate file and
topology file.



WARNING 1 [file 111-87-5.top, line 15]:
 Overriding atomtype h1


WARNING 2 [file 111-87-5.top, line 17]:
 Overriding atomtype c3


WARNING 3 [file 111-87-5.top, line 19]:
 Overriding atomtype ho

It appears that you have somehow duplicated atom types and they are
overriding each other.

Generated 4656 of the 4656 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 4656 of the 4656 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type '1-octanol'
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
Excluding 3 bonded neighbours molecule type '1-octanol'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file topol.top, line 55]:
 System has non-zero total charge: -9.999989e-01

Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (box_oct_sol.gro, 54297)
            does not match topology (topol.top, 54324)
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors

Did you follow the link?  Surely you would have found:

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

-Justin

######################################################################3
this is how I included the itp for the octane molecule in .top file

; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"
#include "octane.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Ion_chain_A2.itp"

; Include water topology
#include "amber99sb-ildn.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
  1    1       1000       1000       1000
#endif

; Include topology for ions
#include "amber99sb-ildn.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Ion_chain_A2        1
1-octanol         1
SOL               565
SOL              8495
#########################################################################

-------------------------------------------------------

Please provide your comments.

On Tue, Mar 27, 2012 at 03:20, Justin A. Lemkul <[email protected]> wrote:


bipin singh wrote:

Thanks for your reply.

Yes, you are right that these topologies are self supporting and there
is no need to to call any other information. I followed your
suggestions and able to generate a biphasic system of water/octane
containing a protein molecule. But, when I tried grompp on this
biphasic system (containing octane+water+protein), it results in error
even if I include the topologies in forcefield.itp file.

The error was

Fatal error:
Atomtype hc not found
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors

If you introduce a new atomtype in your topology somewhere (presumably in
one of the GAFF topologies), then you have to declare them in an
[atomtypes]
directive in the appropriate place in the .top file.  These types are
case
sensitive as well.  For dealing with GAFF-type topologies, assuming you
can
#include them within whatever AMBER force field you've chosen (up to you
to
prove), you can do something like:

#include "amberXX.ff/forcefield.itp"

#include "ligand.itp"

[ moleculetype ]
;name       nrexcl
Protein     3

(etc)

The inclusion of the ligand topology (at this specific location) will add
the new [atomtypes] at the appropriate level of precedence, before any
[moleculetypes] are declared.


-Justin

On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul <[email protected]> wrote:


bipin singh wrote:

Thanks for your reply.
But as far as I understood, in order to use these GAFF topology (for
e.g. to perform simulation using these topologies) with Gromacs we
have to incorporate the information from these topologies to the
existing Amber forcefields in Gromacs or Is there anyway (Possibility
of using Standalone GAFF parameters in Gromacs) to do it without
performing this task.

As David said, the topologies stand on their own.  You do not need to
call
any further information from anywhere.  The .top that you downloaded
begins
with a [defaults] directive, declares atom types, and proceeds through
the
rest of the topology with explicit parameters.

As you said these topologies are self supporting and we do not need to
change ffbonded.itp, but during grompp I got the following error, may
be because I have not added the dihedral information.

ERROR [file oct.top]:
 No default Proper Dih. types

Please provide your suggestions.

I certainly don't see how this could have happened.  All the dihedral
parameters are listed explicitly.  The fatal error should have printed
a
line number in the .top that is problematic, so start by investigating
there.  If you have modified the topology in any way, then undo the
changes
and try again.

I did not have any trouble using this .top in an unmodified form, so I
suspect you've altered it in some way that has broken it.

-Justin

On Mon, Mar 26, 2012 at 17:29, David van der Spoel
<[email protected]>
wrote:

On 2012-03-26 13:55, bipin singh wrote:

Hello all,

I am using the GAFF topology provided for octan-1-ol at Gromacs
liquid
database (http://virtualchemistry.org/molecules/111-87-5/index.php).
I
have incorporated all the parameters
for atoms, bonds and non-bonded interaction type in the forcefield
(Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top),  but
I
am not sure how to add the dihedraltypes information in ffbonded.itp
from the GAFF topology as to add this information I need the phase
and
kd for each dihedral. Is this information is available in the GAFF
topology provided in the Gromacs database ?

This topology is self supporting and you do not need anything else in
ffbonded.itp.

You should be careful merging such parameters with an existing force
field,
because strictly speaking these are different force fields.

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
[email protected]    http://folding.bmc.uu.se
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
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Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

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