Re: [gmx-users] Need to confirm parameters.

[Justin Lemkul]

On 5/31/17 2:26 AM, Sailesh Bataju wrote:

Extract the coordinates of any valine side chain in a protein, make an IBUT .hdb
entry based off of it (all you'll need to do is change 2 -> 3 in the number of H
added to the CB atom) and submit to pdb2gmx; it will build any missing H atoms
for you.



-Justin


I did exactly you said and topology files were generated. The output
of the terminal is:

Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.r2b
Reading test2_edited.pdb...
Read 'ALKANE ISOMER OF N-BUTANE', 13 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 13 atoms

   chain  #res #atoms
   1 'A' 1 13

All occupancies are one
Opening force field file /usr/share/gromacs/top/charmm36.ff/atomtypes.atp
Atomtype 412
Reading residue database... (charmm36)
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.rtp
Residue 1025
Sorting it all out...
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.5#
Processing chain 1 'A' (13 atoms, 1 residues)
Warning: Starting residue IBU1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.arn
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 14 atoms
Making bonds...
Number of bonds was 13, now 13
Generating angles, dihedrals and pairs...
Before cleaning: 27 pairs
Before cleaning: 27 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are   27 dihedrals,0 impropers,   24 angles
 27 pairs,   13 bonds and 0 virtual sites
Total mass 58.124 a.m.u.
Total charge 0.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.1#

Writing coordinate file...
- PLEASE NOTE 
You have successfully generated a topology from: test2_edited.pdb.
The Charmm36 force field and the tip3p water model are used.
- ETON ESAELP 

But the topol.top file looks empty. The topol.top file is:

; Include forcefield parameters
#include "charmm36.ff/forcefield.itp"

[ moleculetype ]
; Namenrexcl
Alkane_chain_A  3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
; residue   1 IBU rtp IBU  q  0.0
  1  CC31A  1IBU CT  1  -0.09 12.011
; qtot -0.09
  2  HCA1A  1IBU HT  2   0.09  1.008   ; qtot 0
  3  CC33A  1IBU C1  3  -0.27 12.011
; qtot -0.27
  4  HCA3A  1IBUH11  4   0.09  1.008
; qtot -0.18
  5  HCA3A  1IBUH12  5   0.09  1.008
; qtot -0.09
  6  HCA3A  1IBUH13  6   0.09  1.008   ; qtot 0
  7  CC33A  1IBU C2  7  -0.27 12.011
; qtot -0.27
  8  HCA3A  1IBUH21  8   0.09  1.008
; qtot -0.18
  9  HCA3A  1IBUH22  9   0.09  1.008
; qtot -0.09
 10  HCA3A  1IBUH23 10   0.09  1.008   ; qtot 0
 11  CC33A  1IBU C3 11  -0.27 12.011
; qtot -0.27
 12  HCA3A  1IBUH31 12   0.09  1.008
; qtot -0.18
 13  HCA3A  1IBUH32 13   0.09  1.008
; qtot -0.09
 14  HCA3A  1IBUH33 14   0.09  1.008   ; qtot 0

[ bonds ]
;  aiaj functc0c1c2c3
 1 2 1
 1 3 1
 1 7 1
 111 1
 3 4 1
 3 5 1
 3 6 1
 7 8 1
 7 9 1
 710 1
1112 1
1113 1
1114 1

[ pairs ]
;  aiaj functc0c1c2c3
 2 4 1
 2 5 1
 2 6 1
 2 8 1
 2 9 1
 210 1
 212 1
 213 1
 214 1
 3 8 1
 3 9 1
 310 1
 312 1
 313 1
 314 1
 4 7 1
 411 1
 5 7 1
 511 1
 6 7 1
 611 1
 712 1
 713 1
 714 1
 811 1
 911 1
1011 1

[ angles ]
;  aiajak funct  

Re: [gmx-users] Need to confirm parameters.

[Sailesh Bataju]

>Extract the coordinates of any valine side chain in a protein, make an IBUT 
>.hdb
>entry based off of it (all you'll need to do is change 2 -> 3 in the number of 
>H
>added to the CB atom) and submit to pdb2gmx; it will build any missing H atoms
>for you.

>-Justin

I did exactly you said and topology files were generated. The output
of the terminal is:

Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.r2b
Reading test2_edited.pdb...
Read 'ALKANE ISOMER OF N-BUTANE', 13 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 13 atoms

  chain  #res #atoms
  1 'A' 1 13

All occupancies are one
Opening force field file /usr/share/gromacs/top/charmm36.ff/atomtypes.atp
Atomtype 412
Reading residue database... (charmm36)
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.rtp
Residue 1025
Sorting it all out...
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.5#
Processing chain 1 'A' (13 atoms, 1 residues)
Warning: Starting residue IBU1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.arn
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 14 atoms
Making bonds...
Number of bonds was 13, now 13
Generating angles, dihedrals and pairs...
Before cleaning: 27 pairs
Before cleaning: 27 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are   27 dihedrals,0 impropers,   24 angles
27 pairs,   13 bonds and 0 virtual sites
Total mass 58.124 a.m.u.
Total charge 0.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.1#

Writing coordinate file...
- PLEASE NOTE 
You have successfully generated a topology from: test2_edited.pdb.
The Charmm36 force field and the tip3p water model are used.
- ETON ESAELP 

But the topol.top file looks empty. The topol.top file is:

; Include forcefield parameters
#include "charmm36.ff/forcefield.itp"

[ moleculetype ]
; Namenrexcl
Alkane_chain_A  3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
; residue   1 IBU rtp IBU  q  0.0
 1  CC31A  1IBU CT  1  -0.09 12.011
; qtot -0.09
 2  HCA1A  1IBU HT  2   0.09  1.008   ; qtot 0
 3  CC33A  1IBU C1  3  -0.27 12.011
; qtot -0.27
 4  HCA3A  1IBUH11  4   0.09  1.008
; qtot -0.18
 5  HCA3A  1IBUH12  5   0.09  1.008
; qtot -0.09
 6  HCA3A  1IBUH13  6   0.09  1.008   ; qtot 0
 7  CC33A  1IBU C2  7  -0.27 12.011
; qtot -0.27
 8  HCA3A  1IBUH21  8   0.09  1.008
; qtot -0.18
 9  HCA3A  1IBUH22  9   0.09  1.008
; qtot -0.09
10  HCA3A  1IBUH23 10   0.09  1.008   ; qtot 0
11  CC33A  1IBU C3 11  -0.27 12.011
; qtot -0.27
12  HCA3A  1IBUH31 12   0.09  1.008
; qtot -0.18
13  HCA3A  1IBUH32 13   0.09  1.008
; qtot -0.09
14  HCA3A  1IBUH33 14   0.09  1.008   ; qtot 0

[ bonds ]
;  aiaj functc0c1c2c3
1 2 1
1 3 1
1 7 1
111 1
3 4 1
3 5 1
3 6 1
7 8 1
7 9 1
710 1
   1112 1
   1113 1
   1114 1

[ pairs ]
;  aiaj functc0c1c2c3
2 4 1
2 5 1
2 6 1
2 8 1
2 9 1
210 1
212 1
213 1
214 1
3 8 1
3 9 1
310 1
312 1
313 1
314 1
4 7 1
411 1
5 7 1
511 1
6 7 1
611 1
712 1
713 1
714 1
811 1
911 1
   1011 1

[ angles ]
;  aiajak functc0c1c2c3
2 1 3 5
2 1 7 

Re: [gmx-users] Need to confirm parameters.

[Justin Lemkul]

On 5/23/17 11:06 PM, Sailesh Bataju wrote:

* Making bonds...

*>>* Warning: Short Bond (5-1 = 0.025 nm)
*>>* Warning: Long Bond (5-6 = 0.99084 nm)
*>>* Warning: Long Bond (1-2 = 0.944378 nm)
*>>* Warning: Long Bond (1-3 = 0.895661 nm)
*>>* Warning: Long Bond (1-4 = 0.866986 nm)
*>>* Warning: Long Bond (7-8 = 0.502204 nm)
*>>* Warning: Long Bond (7-9 = 0.567317 nm)
*>> *Warning: Long Bond (7-10 = 0.92202 nm)
*>>* Warning: Long Bond (11-12 = 0.592831 nm)
*>>* Warning: Long Bond (11-13 = 0.700231 nm)
*>>* Warning: Long Bond (11-14 = 0.729592 nm)*


The short bond warnings do, however, indicate that the starting geometry is bad.



-Justin


I'd a doubt about it you eventually pointed it out sir, thank you.
Those bond lengths have drastic differences than the bond lengths
given in ffbonded.itp file. Here it goes according to the .itp file:-

1-5 = 0.1538 nm

5-6 = 0. nm

1-2 = 0. nm

and so on...

Nothing has matched with those generated bonds. It looks like I've to
modify pdb file manually for correct geometry using distance formula
or is there some other way to do it, sir?



Extract the coordinates of any valine side chain in a protein, make an IBUT .hdb 
entry based off of it (all you'll need to do is change 2 -> 3 in the number of H 
added to the CB atom) and submit to pdb2gmx; it will build any missing H atoms 
for you.


-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] Need to confirm parameters.

[Sailesh Bataju]

>>* Making bonds...
*>>* Warning: Short Bond (5-1 = 0.025 nm)
*>>* Warning: Long Bond (5-6 = 0.99084 nm)
*>>* Warning: Long Bond (1-2 = 0.944378 nm)
*>>* Warning: Long Bond (1-3 = 0.895661 nm)
*>>* Warning: Long Bond (1-4 = 0.866986 nm)
*>>* Warning: Long Bond (7-8 = 0.502204 nm)
*>>* Warning: Long Bond (7-9 = 0.567317 nm)
*>> *Warning: Long Bond (7-10 = 0.92202 nm)
*>>* Warning: Long Bond (11-12 = 0.592831 nm)
*>>* Warning: Long Bond (11-13 = 0.700231 nm)
*>>* Warning: Long Bond (11-14 = 0.729592 nm)*

> The short bond warnings do, however, indicate that the starting geometry is 
> bad.

> -Justin

I'd a doubt about it you eventually pointed it out sir, thank you.
Those bond lengths have drastic differences than the bond lengths
given in ffbonded.itp file. Here it goes according to the .itp file:-

1-5 = 0.1538 nm

5-6 = 0. nm

1-2 = 0. nm

and so on...

Nothing has matched with those generated bonds. It looks like I've to
modify pdb file manually for correct geometry using distance formula
or is there some other way to do it, sir?

Thank you very much.
-- 
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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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Need to confirm parameters.

[Justin Lemkul]

On 5/23/17 8:03 AM, Sailesh Bataju wrote:

The easiest thing to do
(solving this issue and #1) is to create an isobutane .rtp entry and have
pdb2gmx do all the work for you.  It's very simple to do.



-Justin


Thank you sir, I've exactly followed your steps. I've created
isobutane.rtp file and modified residuetypes.dat file by adding IBUT
as Protein and then created PDB file from prodrg server. Then using
pdb2gmx command finally got this result:

Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.r2b
Reading prodrg_ibut.pdb...
WARNING: all CONECT records are ignored
Read 14 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 14 atoms

  chain  #res #atoms
  1 ' ' 1 14


WARNING: there were 4 atoms with zero occupancy and 8 atoms with
 occupancy unequal to one (out of 14 atoms). Check your pdb file.

Opening force field file /usr/share/gromacs/top/charmm36.ff/atomtypes.atp
Atomtype 412
Reading residue database... (charmm36)
Opening force field file /usr/share/gromacs/top/charmm36.ff/isobutane.rtp
Residue 1
Sorting it all out...
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.c.tdb
Processing chain 1 (14 atoms, 1 residues)
Identified residue IBUT0 as a starting terminus.
Identified residue IBUT0 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
No suitable end (N or 5') terminus found in database - assuming this residue
is already in a terminus-specific form and skipping terminus selection.
No suitable end (C or 3') terminus found in database - assuming this residue
is already in a terminus-specific form and skipping terminus selection.
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.arn
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 14 atoms
Making bonds...
Warning: Short Bond (5-1 = 0.025 nm)
Warning: Long Bond (5-6 = 0.99084 nm)
Warning: Long Bond (1-2 = 0.944378 nm)
Warning: Long Bond (1-3 = 0.895661 nm)
Warning: Long Bond (1-4 = 0.866986 nm)
Warning: Long Bond (7-8 = 0.502204 nm)
Warning: Long Bond (7-9 = 0.567317 nm)
Warning: Long Bond (7-10 = 0.92202 nm)
Warning: Long Bond (11-12 = 0.592831 nm)
Warning: Long Bond (11-13 = 0.700231 nm)
Warning: Long Bond (11-14 = 0.729592 nm)
Number of bonds was 13, now 13
Generating angles, dihedrals and pairs...
Before cleaning: 27 pairs
Before cleaning: 27 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are   27 dihedrals,0 impropers,   24 angles
27 pairs,   13 bonds and 0 virtual sites
Total mass 58.124 a.m.u.
Total charge 0.000 e
Writing topology

Writing coordinate file...
- PLEASE NOTE 
You have successfully generated a topology from: prodrg_ibut.pdb.
The Charmm36 force field is used.
- ETON ESAELP 


1. According to the first warning like this "there were 4 atoms with
zero occupancy and 8 atoms with  occupancy unequal to one (out of 14
atoms)"

Is that a kind of error. Did I do any mistake as it said?



That's not an error and is irrelevant.

The short bond warnings do, however, indicate that the starting geometry is bad.


2. If i don't add IBUT as Protein in residuetypes.dat file I get error
like this however I get same topol.top file.

"Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 (14 atoms, 1 residues)
Warning: Starting residue IBUT0 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

---
Program: gmx pdb2gmx, version 2016.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 649)

Fatal error:
Residue 'IBUT' not found in residue topology database"

I've no idea whether I've successfully generated those files.



This fatal error has nothing to do with residuetypes.dat - it says that IBUT is 
not in the .rtp file.  But the above text says it completed successfully.  You 
don't need to denote IBUT as Protein, but there's no harm either way.


-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

==
--

Re: [gmx-users] Need to confirm parameters.

[Sailesh Bataju]

>The easiest thing to do
>(solving this issue and #1) is to create an isobutane .rtp entry and have
>pdb2gmx do all the work for you.  It's very simple to do.

> -Justin

Thank you sir, I've exactly followed your steps. I've created
isobutane.rtp file and modified residuetypes.dat file by adding IBUT
as Protein and then created PDB file from prodrg server. Then using
pdb2gmx command finally got this result:

Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.r2b
Reading prodrg_ibut.pdb...
WARNING: all CONECT records are ignored
Read 14 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 14 atoms

  chain  #res #atoms
  1 ' ' 1 14


WARNING: there were 4 atoms with zero occupancy and 8 atoms with
 occupancy unequal to one (out of 14 atoms). Check your pdb file.

Opening force field file /usr/share/gromacs/top/charmm36.ff/atomtypes.atp
Atomtype 412
Reading residue database... (charmm36)
Opening force field file /usr/share/gromacs/top/charmm36.ff/isobutane.rtp
Residue 1
Sorting it all out...
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.c.tdb
Processing chain 1 (14 atoms, 1 residues)
Identified residue IBUT0 as a starting terminus.
Identified residue IBUT0 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
No suitable end (N or 5') terminus found in database - assuming this residue
is already in a terminus-specific form and skipping terminus selection.
No suitable end (C or 3') terminus found in database - assuming this residue
is already in a terminus-specific form and skipping terminus selection.
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.arn
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 14 atoms
Making bonds...
Warning: Short Bond (5-1 = 0.025 nm)
Warning: Long Bond (5-6 = 0.99084 nm)
Warning: Long Bond (1-2 = 0.944378 nm)
Warning: Long Bond (1-3 = 0.895661 nm)
Warning: Long Bond (1-4 = 0.866986 nm)
Warning: Long Bond (7-8 = 0.502204 nm)
Warning: Long Bond (7-9 = 0.567317 nm)
Warning: Long Bond (7-10 = 0.92202 nm)
Warning: Long Bond (11-12 = 0.592831 nm)
Warning: Long Bond (11-13 = 0.700231 nm)
Warning: Long Bond (11-14 = 0.729592 nm)
Number of bonds was 13, now 13
Generating angles, dihedrals and pairs...
Before cleaning: 27 pairs
Before cleaning: 27 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are   27 dihedrals,0 impropers,   24 angles
27 pairs,   13 bonds and 0 virtual sites
Total mass 58.124 a.m.u.
Total charge 0.000 e
Writing topology

Writing coordinate file...
- PLEASE NOTE 
You have successfully generated a topology from: prodrg_ibut.pdb.
The Charmm36 force field is used.
- ETON ESAELP 


1. According to the first warning like this "there were 4 atoms with
zero occupancy and 8 atoms with  occupancy unequal to one (out of 14
atoms)"

Is that a kind of error. Did I do any mistake as it said?

2. If i don't add IBUT as Protein in residuetypes.dat file I get error
like this however I get same topol.top file.

"Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 (14 atoms, 1 residues)
Warning: Starting residue IBUT0 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

---
Program: gmx pdb2gmx, version 2016.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 649)

Fatal error:
Residue 'IBUT' not found in residue topology database"

I've no idea whether I've successfully generated those files.

Thank you very much.
-- 
Gromacs Users mailing list

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Re: [gmx-users] Need to confirm parameters.

[Justin Lemkul]

On 5/22/17 10:00 AM, Sailesh Bataju wrote:

Hi Sir,

Right, CHARMM force field is what I'm looking for. Thank you very much
sir for your advice. I've made parameter file of isobutane using
CHARMM36 force field files shown below so I've a few questions
regarding it.

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  1 1   yes 1.0 1.0

[ atomtypes ]
;   name  at.num   masscharge ptype   sigma epsilon
   CC31A 612.011000   -0.090A   0.356359487256  0.13389
   CC33A 612.011000   -0.270A   0.363486677001  0.32635
   HCA1A 1 1.0080000.090A   0.238760856462  0.18828
   HCA3A 1 1.0080000.090A   0.238760856462  0.10042

[ moleculetype ]
; Namenrexcl
isobutane   3

[ atoms ]
;   nr  typeresnr   residue atomcgnrcharge  mass
typeBchargeB  massB
; residue   1 IBUT rtp IBUT q  0.0
1   CC33A   1   IBUTC1  1   -0.270  ; qtot
-0.270
2   HCA3A   1   IBUTH2  20.090  ; qtot -0.180
3   HCA3A   1   IBUTH3  30.090  ; qtot -0.090
4   HCA3A   1   IBUTH4  40.090  ; qtot  0.000
5   CC31A   1   IBUTC5  5   -0.090  ; qtot -0.090
6   HCA1A   1   IBUTH6  60.090  ; qtot  0.000
7   CC33A   1   IBUTC7  7   -0.270  ; qtot -0.270
8   HCA3A   1   IBUTH8  80.090  ; qtot -0.180
9   HCA3A   1   IBUTH9  90.090  ; qtot -0.090
10  HCA3A   1   IBUTH10 10   0.090  ; qtot  0.000
11  CC33A   1   IBUTC11 11  -0.270  ; qtot -0.270
12  HCA3A   1   IBUTH12 12   0.090  ; qtot -0.180
13  HCA3A   1   IBUTH13 13   0.090  ; qtot -0.090
14  HCA3A   1   IBUTH14 14   0.090  ; qtot  0.000

[ bonds ]
:   ai  aj  funct   b0(nm)  kb[KJ mol^(-1) nm^(-2)] ; 13 bonds
1   2   1   0.  269449.60
1   3   1   0.  269449.60
1   4   1   0.  269449.60   ;
 C13
1   5   1   0.1538  186188.00   ;
 |
5   6   1   0.  258571.20   ;
H14--C11--H12
5   7   1   0.1538  186188.00   ;
 |
5   11  1   0.1538  186188.00   ;
 H2  |   H8
7   8   1   0.  269449.60   ;
 |   |   |
7   9   1   0.  269449.60   ;
 H3--C1--C5--C7--H9
7   10  1   0.  269449.60   ;
 |   |   |
11  12  1   0.  269449.60   ;
 H4  H6  H10
11  13  1   0.  269449.60   ;
11  14  1   0.  269449.60

[ pairs ]
;ai aj funct; 27 pairs
 1  8  1
 1  9  1
 1 10  1
 1 12  1
 1 13  1
 1 14  1
 2  6  1
 2  7  1
 2 11  1
 3  6  1
 3  7  1
 3 11  1
 4  6  1
 4  7  1
 4 11  1
 6  8  1
 6  9  1
 6 10  1
 6 12  1
 6 13  1
 6 14  1
 7 12  1
 7 13  1
 7 14  1
 8 11  1
 9 11  1
10 11  1

[ angles ]
;  ai   aj  ak  funct   theta0(deg) ktheta(KJ mol^(-1) rad^(-2))
 ub0(nm)  kub(KJ mol^(-1) nm^(-2)) ; 24 angles
2   1   3   5   108.40  297.064000
 0.1802   4518.72; HCA3A-CC33A-HCA3A
2   1   4   5   108.40  297.064000
 0.1802   4518.72
3   1   4   5   108.40  297.064000
 0.1802   4518.72
8   7   9   5   108.40  297.064000
 0.1802   4518.72
8   7   10  5   108.40  297.064000
 0.1802   4518.72
9   7   10  5   108.40  297.064000
 0.1802   4518.72
12  11  13  5   108.40  297.064000
 0.1802   4518.72
12  11  14  5   108.40  297.064000
 0.1802   4518.72
13  11  14  5   108.40  297.064000
 0.1802   4518.72
5   1   2   5   110.10  279.742240
 0.2179   18853.10   ; CC31A-CC33A-HCA3A
5   1   3   5   110.10  279.742240
 0.2179   18853.10
5   1   4   5   110.10  279.742240
 0.2179   18853.10
5   7   8   5   110.10  279.742240
 0.2179   18853.10
5   7   9   5   110.10  

Re: [gmx-users] Need to confirm parameters.

[Sailesh Bataju]

Hi Sir,

Right, CHARMM force field is what I'm looking for. Thank you very much
sir for your advice. I've made parameter file of isobutane using
CHARMM36 force field files shown below so I've a few questions
regarding it.

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  1 1   yes 1.0 1.0

[ atomtypes ]
;   name  at.num   masscharge ptype   sigma epsilon
   CC31A 612.011000   -0.090A   0.356359487256  0.13389
   CC33A 612.011000   -0.270A   0.363486677001  0.32635
   HCA1A 1 1.0080000.090A   0.238760856462  0.18828
   HCA3A 1 1.0080000.090A   0.238760856462  0.10042

[ moleculetype ]
; Namenrexcl
isobutane   3

[ atoms ]
;   nr  typeresnr   residue atomcgnrcharge  mass
typeBchargeB  massB
; residue   1 IBUT rtp IBUT q  0.0
1   CC33A   1   IBUTC1  1   -0.270  ; qtot
-0.270
2   HCA3A   1   IBUTH2  20.090  ; qtot -0.180
3   HCA3A   1   IBUTH3  30.090  ; qtot -0.090
4   HCA3A   1   IBUTH4  40.090  ; qtot  0.000
5   CC31A   1   IBUTC5  5   -0.090  ; qtot -0.090
6   HCA1A   1   IBUTH6  60.090  ; qtot  0.000
7   CC33A   1   IBUTC7  7   -0.270  ; qtot -0.270
8   HCA3A   1   IBUTH8  80.090  ; qtot -0.180
9   HCA3A   1   IBUTH9  90.090  ; qtot -0.090
10  HCA3A   1   IBUTH10 10   0.090  ; qtot  0.000
11  CC33A   1   IBUTC11 11  -0.270  ; qtot -0.270
12  HCA3A   1   IBUTH12 12   0.090  ; qtot -0.180
13  HCA3A   1   IBUTH13 13   0.090  ; qtot -0.090
14  HCA3A   1   IBUTH14 14   0.090  ; qtot  0.000

[ bonds ]
:   ai  aj  funct   b0(nm)  kb[KJ mol^(-1) nm^(-2)] ; 13 bonds
1   2   1   0.  269449.60
1   3   1   0.  269449.60
1   4   1   0.  269449.60   ;
 C13
1   5   1   0.1538  186188.00   ;
 |
5   6   1   0.  258571.20   ;
H14--C11--H12
5   7   1   0.1538  186188.00   ;
 |
5   11  1   0.1538  186188.00   ;
 H2  |   H8
7   8   1   0.  269449.60   ;
 |   |   |
7   9   1   0.  269449.60   ;
 H3--C1--C5--C7--H9
7   10  1   0.  269449.60   ;
 |   |   |
11  12  1   0.  269449.60   ;
 H4  H6  H10
11  13  1   0.  269449.60   ;
11  14  1   0.  269449.60

[ pairs ]
;ai aj funct; 27 pairs
 1  8  1
 1  9  1
 1 10  1
 1 12  1
 1 13  1
 1 14  1
 2  6  1
 2  7  1
 2 11  1
 3  6  1
 3  7  1
 3 11  1
 4  6  1
 4  7  1
 4 11  1
 6  8  1
 6  9  1
 6 10  1
 6 12  1
 6 13  1
 6 14  1
 7 12  1
 7 13  1
 7 14  1
 8 11  1
 9 11  1
10 11  1

[ angles ]
;  ai   aj  ak  funct   theta0(deg) ktheta(KJ mol^(-1) rad^(-2))
 ub0(nm)  kub(KJ mol^(-1) nm^(-2)) ; 24 angles
2   1   3   5   108.40  297.064000
 0.1802   4518.72; HCA3A-CC33A-HCA3A
2   1   4   5   108.40  297.064000
 0.1802   4518.72
3   1   4   5   108.40  297.064000
 0.1802   4518.72
8   7   9   5   108.40  297.064000
 0.1802   4518.72
8   7   10  5   108.40  297.064000
 0.1802   4518.72
9   7   10  5   108.40  297.064000
 0.1802   4518.72
12  11  13  5   108.40  297.064000
 0.1802   4518.72
12  11  14  5   108.40  297.064000
 0.1802   4518.72
13  11  14  5   108.40  297.064000
 0.1802   4518.72
5   1   2   5   110.10  279.742240
 0.2179   18853.10   ; CC31A-CC33A-HCA3A
5   1   3   5   110.10  279.742240
 0.2179   18853.10
5   1   4   5   110.10  279.742240
 0.2179   18853.10
5   7   8   5   110.10  279.742240
 0.2179   18853.10
5   7   9   5   110.10  279.742240
 0.2179   18853.10
5   7  

Re: [gmx-users] Need to confirm parameters.

[Justin Lemkul]

On 5/19/17 8:22 AM, Sailesh Bataju wrote:

Hi Sir,

You mean like choosing OPLS forcefield for all-atom model would be moer
appropriate for me?



At minimum, some all-atom force field, because whatever you were doing before 
has no relationship to GROMOS and is unlikely to succeed.


Isobutane is just the valine side chain, so that's certainly a model compound in 
existing force fields and should have parameters published and validated for any 
of the major all-atom force fields.  I know it's in CHARMM, and certainly others.


-Justin


Thank you.

On Fri, May 19, 2017 at 5:15 PM, Sailesh Bataju  wrote:


Hi Sir/Ma'am,

I've finally created parameter file of isobutane using gromos54a7
forcefield for all-atom model. Some of the parameters for bond angle
parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
file in the relevant forcefield, instead I used FTFE  -  CTFE  -  FTFE and
CLChl  - CChl  - CLChl respectively which i found it in the sample of the
file generated by https://atb.uq.edu.au/ website. Somehow luckily found
corresponding bond angle approximately equivalent to the experimental data
observed but didn't find the bond angle constant in experimental data.
Therefore I'm not sure if I can trust the parameter selected.

I need your advice to help me decide to go further.
Thank you very much.

--
Self-reliant is the great potential for success.







--
==

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] Need to confirm parameters.

[Sailesh Bataju]

Hi Sir,

You mean like choosing OPLS forcefield for all-atom model would be moer
appropriate for me?

Thank you.

On Fri, May 19, 2017 at 5:15 PM, Sailesh Bataju  wrote:

> Hi Sir/Ma'am,
>
> I've finally created parameter file of isobutane using gromos54a7
> forcefield for all-atom model. Some of the parameters for bond angle
> parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
> file in the relevant forcefield, instead I used FTFE  -  CTFE  -  FTFE and
> CLChl  - CChl  - CLChl respectively which i found it in the sample of the
> file generated by https://atb.uq.edu.au/ website. Somehow luckily found
> corresponding bond angle approximately equivalent to the experimental data
> observed but didn't find the bond angle constant in experimental data.
> Therefore I'm not sure if I can trust the parameter selected.
>
> I need your advice to help me decide to go further.
> Thank you very much.
>
> --
> Self-reliant is the great potential for success.
>



-- 
Self-reliant is the great potential for success.
-- 
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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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Need to confirm parameters.

[Justin Lemkul]

On 5/19/17 7:30 AM, Sailesh Bataju wrote:

Hi Sir/Ma'am,

I've finally created parameter file of isobutane using gromos54a7
forcefield for all-atom model. Some of the parameters for bond angle
parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
file in the relevant forcefield, instead I used FTFE  -  CTFE  -  FTFE and
CLChl  - CChl  - CLChl respectively which i found it in the sample of the
file generated by https://atb.uq.edu.au/ website. Somehow luckily found
corresponding bond angle approximately equivalent to the experimental data
observed but didn't find the bond angle constant in experimental data.
Therefore I'm not sure if I can trust the parameter selected.



GROMOS force fields are united-atom so isobutane will have no H atoms.  Use a 
sensible all-atom model as your starting point, because any of them will have 
the actual parameters you need rather than trying to rely on halogens as analogs 
of H atoms.


-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!

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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Need to confirm parameters.

[Sailesh Bataju]

Hi Sir/Ma'am,

I've finally created parameter file of isobutane using gromos54a7
forcefield for all-atom model. Some of the parameters for bond angle
parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
file in the relevant forcefield, instead I used FTFE  -  CTFE  -  FTFE and
CLChl  - CChl  - CLChl respectively which i found it in the sample of the
file generated by https://atb.uq.edu.au/ website. Somehow luckily found
corresponding bond angle approximately equivalent to the experimental data
observed but didn't find the bond angle constant in experimental data.
Therefore I'm not sure if I can trust the parameter selected.

I need your advice to help me decide to go further.
Thank you very much.

-- 
Self-reliant is the great potential for success.
-- 
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.