Re: [gmx-users] add parameter

[Malihe Hasanzadeh]

Dear Justin,
Thank you for your reply. I have parameters from some manuscript and add
all of them in force field. There is two parts of dihedral types in
ffbonded.itp that one of them has func=4 and another has func=9. Also I
have two types of parameters for dihedral;* Proper* and* Improper *dihedral
that the proper types have* scale=1, 2 or 3 *and* periodicity=**1, 2
or 3. *Since
some of *Proper types* are the same with different Phase, V and Periodicity
number, so I think, I should add all of them ( proper and improper
parameters) in second part with func=9 and ignore scale number for *Proper
types*. Because when I add them in first part with func=4 gave error. I see
manual but I couldn't find where do I add them.

for example:

*Proper types*
dihedral types   scaling  phase
V(kj/mol)periodicity

O   C   OQ  HQ 1   0.0  7.9496
 1  ;
O   C   OQ  HQ 1180.0  9.6232
2  ;

*Improper types*
dihedral types phase
V(kj/mol)periodicity

CA   CA   C  HQ 180.0  9.6232
2  ;

Could you please help me , where do I add the parameters of proper and
improper types in forcefield and what is the func number for them?
Thanks
Malihe







On Fri, Feb 12, 2016 at 5:12 AM, Justin Lemkul  wrote:

>
>
> On 2/11/16 12:03 PM, Malihe Hasanzadeh wrote:
>
>> Hi
>> I have three water molecules and one new residue that I want to add their
>> parameters to force field Amber99sb. One of water molecules has only one
>> hydrogen, and since I want to prevent from replacing with SOL in solvation
>> step, So I define them as new residue in .rtp file:
>>
>> [ INN ]
>>   [ atoms ]
>> H1H   0.384620 1
>>  OO  -0.671930 2
>> H2H   0.384620 3
>>
>>
>> [ INT ]
>>   [ atoms ]
>> H1H   0.286310 1
>>  OO  -0.341910 2
>> H2H   0.286310 3
>>
>>
>> [ INB ]
>>   [ atoms ]
>> H1H   0.477860 1
>>  OO  -1.092580 2
>> Also define them in .dat file as Protein  and in .hdb file as below:
>>
>>
> Defining these residues as protein is not necessary.
>
> INN2
>> 17H1O
>> 17H2O
>> INT2
>> 17H1O
>> 17H2O
>> INB1
>> 17H1O
>>
>> But when I start MD simulation(gromacs 5.0.4) in step of mdrun ...em,
>> gives segmentation fault! when I remove their parameters in .hdb file, it
>> is done but without any hydrogen for them, just three oxygen atoms in
>> em.gro!
>>
>>
> This is because you would have had to invoke -missing with pdb2gmx and
> yield something totally useless.
>
> Immediate seg faults are indicative of complete instability.  Note that
> none of your .rtp entries have [bonds] defined, so you probably just have
> particles very close to one another (e.g. as they would be in a real
> molecule) but no covalent attachment, so they likely just fly apart.
>
> Also I have another problem with that new residue, this residue is like a
>> Lys but has two carbonyl groups binded to extra carbon instead of amino
>> group in Lys. So I used Lys parameters for that and add some bonds and
>> atoms to it:
>>
>> [ NEW ] ;
>>   [ atoms ]
>>  N   N
>>  H   H
>> CA   CT
>> HAH1
>> CB   CT
>>HB1   HC
>>HB2   HC
>> CG  CT
>>HG1  H
>>HG2  H
>> CD  CT
>>HD1  HC
>>HD2  HC
>> CE  CT
>>HE1  HP
>>HE2  HP
>> NZ  N
>> HZ  H
>> CX  C
>>OQ1 O
>>OQ2 O
>>  C  C
>>  O  O
>>   [ bonds ]
>>   N H
>>   NCA
>>  CAHA
>>  CACB
>>  CA C
>>  CB   HB1
>>  CB   HB2
>>  CBCG
>>  CG   HG1
>>  CG   HG2
>>  CGCD
>>  CD   HD1
>>  CD   HD2
>>  CDCE
>>  CE   HE1
>>  CE   HE2
>>  CENZ
>>  NZHZ
>>  NZCX
>>   C O
>>  CX   OQ1
>>  CX   OQ2
>>   [ impropers ]
>>  -CCA N H
>>  CA+N C O
>> when I added only atoms parameters in .rtp file, finally in em.gro file
>> there wasn't any bond between atoms of new residue and when I added bond
>>
>
> As you should expect.  See above.  [bonds] is a mandatory directive (which
> is also stated clearly in the manual).
>
> parameters also, in grompp gives 10 error about "default angel and
>> dihedral"! I find the number of angels in .top file and added them to
>> ffbonded.itp, but anything have no change.
>>
>
> You're adding moieties that don't exist in the force field, unless you
> have parameters from some external source (e.g. something published or
> otherwise available in a force field repository).
>
> -Justin
>
> --
> 

Re: [gmx-users] add parameter

[Justin Lemkul]

On 2/11/16 12:03 PM, Malihe Hasanzadeh wrote:

Hi
I have three water molecules and one new residue that I want to add their
parameters to force field Amber99sb. One of water molecules has only one
hydrogen, and since I want to prevent from replacing with SOL in solvation
step, So I define them as new residue in .rtp file:

[ INN ]
  [ atoms ]
H1H   0.384620 1
 OO  -0.671930 2
H2H   0.384620 3


[ INT ]
  [ atoms ]
H1H   0.286310 1
 OO  -0.341910 2
H2H   0.286310 3


[ INB ]
  [ atoms ]
H1H   0.477860 1
 OO  -1.092580 2
Also define them in .dat file as Protein  and in .hdb file as below:



Defining these residues as protein is not necessary.


INN2
17H1O
17H2O
INT2
17H1O
17H2O
INB1
17H1O

But when I start MD simulation(gromacs 5.0.4) in step of mdrun ...em,
gives segmentation fault! when I remove their parameters in .hdb file, it
is done but without any hydrogen for them, just three oxygen atoms in
em.gro!



This is because you would have had to invoke -missing with pdb2gmx and yield 
something totally useless.


Immediate seg faults are indicative of complete instability.  Note that none of 
your .rtp entries have [bonds] defined, so you probably just have particles very 
close to one another (e.g. as they would be in a real molecule) but no covalent 
attachment, so they likely just fly apart.



Also I have another problem with that new residue, this residue is like a
Lys but has two carbonyl groups binded to extra carbon instead of amino
group in Lys. So I used Lys parameters for that and add some bonds and
atoms to it:

[ NEW ] ;
  [ atoms ]
 N   N
 H   H
CA   CT
HAH1
CB   CT
   HB1   HC
   HB2   HC
CG  CT
   HG1  H
   HG2  H
CD  CT
   HD1  HC
   HD2  HC
CE  CT
   HE1  HP
   HE2  HP
NZ  N
HZ  H
CX  C
   OQ1 O
   OQ2 O
 C  C
 O  O
  [ bonds ]
  N H
  NCA
 CAHA
 CACB
 CA C
 CB   HB1
 CB   HB2
 CBCG
 CG   HG1
 CG   HG2
 CGCD
 CD   HD1
 CD   HD2
 CDCE
 CE   HE1
 CE   HE2
 CENZ
 NZHZ
 NZCX
  C O
 CX   OQ1
 CX   OQ2
  [ impropers ]
 -CCA N H
 CA+N C O
when I added only atoms parameters in .rtp file, finally in em.gro file
there wasn't any bond between atoms of new residue and when I added bond


As you should expect.  See above.  [bonds] is a mandatory directive (which is 
also stated clearly in the manual).



parameters also, in grompp gives 10 error about "default angel and
dihedral"! I find the number of angels in .top file and added them to
ffbonded.itp, but anything have no change.


You're adding moieties that don't exist in the force field, unless you have 
parameters from some external source (e.g. something published or otherwise 
available in a force field repository).


-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] add parameter

[Malihe Hasanzadeh]

Hi
I have three water molecules and one new residue that I want to add their
parameters to force field Amber99sb. One of water molecules has only one
hydrogen, and since I want to prevent from replacing with SOL in solvation
step, So I define them as new residue in .rtp file:

[ INN ]
 [ atoms ]
   H1H   0.384620 1
OO  -0.671930 2
   H2H   0.384620 3


[ INT ]
 [ atoms ]
   H1H   0.286310 1
OO  -0.341910 2
   H2H   0.286310 3


[ INB ]
 [ atoms ]
   H1H   0.477860 1
OO  -1.092580 2
Also define them in .dat file as Protein  and in .hdb file as below:

INN2
17H1O
17H2O
INT2
17H1O
17H2O
INB1
17H1O

But when I start MD simulation(gromacs 5.0.4) in step of mdrun ...em,
gives segmentation fault! when I remove their parameters in .hdb file, it
is done but without any hydrogen for them, just three oxygen atoms in
em.gro!

Also I have another problem with that new residue, this residue is like a
Lys but has two carbonyl groups binded to extra carbon instead of amino
group in Lys. So I used Lys parameters for that and add some bonds and
atoms to it:

[ NEW ] ;
 [ atoms ]
N   N
H   H
   CA   CT
   HAH1
   CB   CT
  HB1   HC
  HB2   HC
   CG  CT
  HG1  H
  HG2  H
   CD  CT
  HD1  HC
  HD2  HC
   CE  CT
  HE1  HP
  HE2  HP
   NZ  N
   HZ  H
   CX  C
  OQ1 O
  OQ2 O
C  C
O  O
 [ bonds ]
 N H
 NCA
CAHA
CACB
CA C
CB   HB1
CB   HB2
CBCG
CG   HG1
CG   HG2
CGCD
CD   HD1
CD   HD2
CDCE
CE   HE1
CE   HE2
CENZ
NZHZ
NZCX
 C O
CX   OQ1
CX   OQ2
 [ impropers ]
-CCA N H
CA+N C O
when I added only atoms parameters in .rtp file, finally in em.gro file
there wasn't any bond between atoms of new residue and when I added bond
parameters also, in grompp gives 10 error about "default angel and
dihedral"! I find the number of angels in .top file and added them to
ffbonded.itp, but anything have no change.
please help me. what is my mistake about these two insistent problems?
Thanks
Malihe
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[gmx-users] add parameter

[Mahnaz Mirsoltani]

Hi
 I want to add some bond parameters in ffbonded.itp file, and
as I read in manual, unit of "kb" is "kj.mol-1.nm-2" and
 unit of "b0" is "nm". But I have these quantities with
 "kcal.mol-1.Å-2" and "Å". How do I convert these? Is it
enough converting of kcal/mol to kj/mol for "kb" and "Å" to
 'nm" for "b0"? 
 Thanks
 Mah
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Re: [gmx-users] add parameter

[Justin Lemkul]

On 2/9/16 5:04 PM, Mahnaz Mirsoltani wrote:

Hi
  I want to add some bond parameters in ffbonded.itp file, and
as I read in manual, unit of "kb" is "kj.mol-1.nm-2" and
  unit of "b0" is "nm". But I have these quantities with
  "kcal.mol-1.Å-2" and "Å". How do I convert these? Is it


Unit transformation is covered in any undergraduate chemistry or physics text 
book.


enough converting of kcal/mol to kj/mol for "kb" and "Å" to
  'nm" for "b0"?


Yes.

-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

* Please search the archive at 
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