Re: [gmx-users] Re: OPLS-AA/L force field

[Justin A. Lemkul]

you zou wrote:

Hi,

Thank you for your help.Now there is this question that I have just .pdb file
and when use protonate command it is" protonate -f drg.pdb -o drg.gro", this
is without hydrogens atoms too.

I think something is wrong, but I don't know what it is.In definition of
"protonate" there is "protonate reads (a) conformation(s) and adds all
missing hydrogens as defined in ffgmx2.hdb
." but I can't add
hydrogens. What is my problem?



Well, your command isn't correct.  The protonate command takes (at minimum) the 
-s flag, not -f (which is optional, and context-dependent, if I recall).


The other fact is that if a residue isn't listed in ffgmx2.hdb, it won't get 
protonated, but it is trivial to add new molecules into the .hdb file with the 
help of the manual.  The syntax for .hdb entries is straightforward.


-Justin


Thanks

you zou wrote:

Hi again,

Sorry, I have one question now, what is the meaning of structure? I think 
coordinates is structure, is it true?




Yes, a coordinate file contains a structure.


If it is true, when I used "editconf -f drg.pdb -o drg.gro" number of atoms
 are different from top file and editconf can not add hydrogens to drg.gro.
If Gromacs can handle .pdb, How can it do this, because number of atoms are
 different(Which command I have to use?). If can't handle it how can I add 
Hydrogens to drg.gro?




The underlying assumption when running any simulation is that you have
developed the proper parameters for the ligand and that it has an appropriate
structure. If you need additional hydrogens, the Gromacs "protonate" tool can
generate an all-atom structure.

-Justin


Thanks,



you zou wrote:

Hi again,

Sorry I confused you with my question. My question is How can I make .gro
 file and .top file from

drug.pdb (that removed from drug-enzyme.pdb)?


If I can use x2top command I will make .top file just, is it true? I
think .gro file is dependent on forcefiled too so If I use editconf
command I will miss something, is it true?


If you want to use x2top, the assumption is that the structure is already 
appropriate as is, that is it is properly protonated. The only tool that is

 smart enough to add force field-specific hydrogens is pdb2gmx. If you're


using OPLS-AA, then you should have all hydrogens present, anyway. If that's
true, then you can use editconf to create a .gro file (which is not 
absolutely necessary; Gromacs can handle .pdb files just fine). If you

don't have all the appropriate atoms present in your molecule's structure,
then you need to build a proper structure.

-Justin



Thank you again


you

zou wrote:

Hi Justin,

Thank you for your help, But when I run x2top command there is one
error that is: " Can not find forcefield for atom C1-1 with 2 bonds Can
not find forcefield for atom C4-4 with 2 bonds ...

&g t; Program x2top, VERSION 4.0.5

Source code file: x2top.c, line: 207

Fatal error: Could only find a f

orcefield type for 6 out of 24 atoms"




Not all of your atom types are described by ffop

lsaa.n2t so you will have

to add them. There are only a limited number of types that are covered by
 default.

http://www.gromacs.org/Documentation/File_Formats/.n2t_File


I don't know how

can I adjust this error. I have one more question again,
this command give me a top file, if I want gro file of this pdb (drug 
that has removed from drug-enzyme complex) how can I do that?




Do you just need a .gro file, and not a .top? My understanding from your
 first message was that you needed a topo logy. If you just need a .gro, 
then simply pass your .pdb file to editconf.


-Justin<

br>>>

you zou wrote:

Dear Users,

I have one question about Drug-Enzyme Complex,Similar to tutorial If
I


want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug

but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg
 Beta version" server too, or not?


No. You can't use two different force fields in

one simulation system.



If I can't use this server, how can I make .gro file and .itp file
for


& gt;>> drug that remove from initial .pdb file?




There are several programs in the User Contributions from the website,
 x2top (which is distributed with Gromacs), or you c

an build the topology

by hand. No matter what you choose, you ne

ed a thorough understanding of the mechanics of

your chosen force field, methods of validation, and of course Chapter 5
 in the

Gromacs manual.




 Your
E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now.




--


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

==

[gmx-users] Re: OPLS-AA/L force field

[you zou]

Hi,Thank you for your help.Now there is this question that I have just .pdb 
file and when use protonate command it is" protonate -f drg.pdb -o drg.gro", 
this is without hydrogens atoms too.I think something is wrong, but I don't 
know what it is.In definition of "protonate" there is "protonate reads (a) 
conformation(s) and adds all missing hydrogens as defined in ffgmx2.hdb." but I 
can't add hydrogens. What is my problem?Thanksyou zou wrote:
> Hi again,
> 
> Sorry, I have one question now, what is the meaning of structure? I think
> coordinates is structure, is it true?
> 

Yes, a coordinate file contains a structure.

> If it is true, when I used "editconf -f drg.pdb -o drg.gro" number of atoms
> are different from top file and editconf can not add hydrogens to drg.gro. If
> Gromacs can handle .pdb, How can it do this, because number of atoms are
> different(Which command I have to use?). If can't handle it how can I add
> Hydrogens to drg.gro?
> 

The underlying assumption when running any simulation is that you have 
developed 
the proper parameters for the ligand and that it has an appropriate structure. 
If you need additional hydrogens, the Gromacs "protonate" tool can generate an 
all-atom structure.

-Justin

> Thanks,
> 
> 
> 
> you zou wrote:
>> Hi again,
>> 
>> Sorry I confused you with my question. My question is How can I make .gro 
>> file and .top file from
> drug.pdb (that removed from drug-enzyme.pdb)?
>> 
>> If I can use x2top command I will make .top file just, is it true? I think 
>> .gro file is dependent on forcefiled too so If I use editconf command I
>> will miss something, is it true?
> 
> If you want to use x2top, the assumption is that the structure is already 
> appropriate as is, that is it is properly protonated. The only tool that is 
> smart enough to add force field-specific hydrogens is pdb2gmx. If you're
> using OPLS-AA, then you should have all hydrogens present, anyway. If that's
> true, then you can use editconf to create a .gro file (which is not
> absolutely necessary; Gromacs can handle .pdb files just fine). If you don't
> have all the appropriate atoms present in your molecule's structure, then you
> need to build a proper structure.
> 
> -Justin
> 
>> 
>> Thank you again
>> 
>> 
>> you
> zou wrote:
>>> Hi Justin,
>>> 
>>> Thank you for your help, But when I run x2top command there is one error
>>> that is: " Can not find forcefield for atom C1-1 with 2 bonds Can not
>>> find forcefield for atom C4-4 with 2 bonds ...
>> &g t; Program x2top, VERSION 4.0.5
>>> Source code file: x2top.c, line: 207
>>> 
>>> Fatal error: Could only find a forcefield type for 6 out of 24 atoms"
>>> 
>> 
>> Not all of your atom types are described by ffoplsaa.n2t so you will have
>> to add them. There are only a limited number of types that are covered by 
>> default.
>> 
>> http://www.gromacs.org/Documentation/File_Formats/.n2t_File
>> 
>>> I don't know how
> can I adjust this error. I have one more question again,
>>> this command give me a top file, if I want gro file of this pdb (drug
>>> that has removed from drug-enzyme complex) how can I do that?
>>> 
>> 
>> Do you just need a .gro file, and not a .top? My understanding from your 
>> first message was that you needed a topo logy. If you just need a .gro,
>> then simply pass your .pdb file to editconf.
>> 
>> -Justin
>> 
>>> you zou wrote:
 Dear Users,
 
 I have one question about Drug-Enzyme Complex,Similar to tutorial If I
 
>>> want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
 but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
 Beta version" server too, or not?
>>> 
>>> No. You can't use two different force fields in
> one simulation system.
>>> 
 If I can't use this server, how can I make .gro file and .itp file for
 
> & gt;>> drug that remove from initial .pdb file?
 
>>> 
>>> There are several programs in the User Contributions from the website, 
>>> x2top (which is distributed with Gromacs), or you can build the topology
>>> by hand. No matter what you choose, you ne
>> ed a thorough understanding of the mechanics of
>>> your chosen force field, methods of validation, and of course Chapter 5
>>> in the
>>> 
>>> Gromacs manual.
>>> 
  
_
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Re: [gmx-users] Re: OPLS-AA/L force field

[Justin A. Lemkul]

you zou wrote:

Hi again,

Sorry, I have one question now, what is the meaning of structure? I think
coordinates is structure, is it true?



Yes, a coordinate file contains a structure.


If it is true, when I used "editconf -f drg.pdb -o drg.gro" number of atoms
are different from top file and editconf can not add hydrogens to drg.gro. If
Gromacs can handle .pdb, How can it do this, because number of atoms are
different(Which command I have to use?). If can't handle it how can I add
Hydrogens to drg.gro?



The underlying assumption when running any simulation is that you have developed 
the proper parameters for the ligand and that it has an appropriate structure. 
If you need additional hydrogens, the Gromacs "protonate" tool can generate an 
all-atom structure.


-Justin


Thanks,



you zou wrote:

Hi again,

Sorry I confused you with my question. My question is How can I make .gro 
file and .top file from

drug.pdb (that removed from drug-enzyme.pdb)?


If I can use x2top command I will make .top file just, is it true? I think 
.gro file is dependent on forcefiled too so If I use editconf command I

will miss something, is it true?


If you want to use x2top, the assumption is that the structure is already 
appropriate as is, that is it is properly protonated. The only tool that is 
smart enough to add force field-specific hydrogens is pdb2gmx. If you're

using OPLS-AA, then you should have all hydrogens present, anyway. If that's
true, then you can use editconf to create a .gro file (which is not
absolutely necessary; Gromacs can handle .pdb files just fine). If you don't
have all the appropriate atoms present in your molecule's structure, then you
need to build a proper structure.

-Justin



Thank you again


you

zou wrote:

Hi Justin,

Thank you for your help, But when I run x2top command there is one error
 that is: " Can not find forcefield for atom C1-1 with 2 bonds Can not
find forcefield for atom C4-4 with 2 bonds ...

&g t; Program x2top, VERSION 4.0.5

Source code file: x2top.c, line: 207

Fatal error: Could only find a forcefield type for 6 out of 24 atoms"



Not all of your atom types are described by ffoplsaa.n2t so you will have
to add them. There are only a limited number of types that are covered by 
default.


http://www.gromacs.org/Documentation/File_Formats/.n2t_File


I don't know how

can I adjust this error. I have one more question again,

this command give me a top file, if I want gro file of this pdb (drug
that has removed from drug-enzyme complex) how can I do that?



Do you just need a .gro file, and not a .top? My understanding from your 
first message was that you needed a topo logy. If you just need a .gro,

then simply pass your .pdb file to editconf.

-Justin


you zou wrote:

Dear Users,

I have one question about Drug-Enzyme Complex,Similar to tutorial If I


want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
Beta version" server too, or not?


No. You can't use two different force fields in

one simulation system.



If I can't use this server, how can I make .gro file and .itp file for


& gt;>> drug that remove from initial .pdb file?




There are several programs in the User Contributions from the website, 
x2top (which is distributed with Gromacs), or you can build the topology

by hand. No matter what you choose, you ne

ed a thorough understanding of the mechanics of

your chosen force field, methods of validation, and of course Chapter 5
in the

Gromacs manual.




 
Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up

 now. 



-


 
Hotmail: Free, trusted and rich email service. Get it now. 





--


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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[gmx-users] Re: OPLS-AA/L force field

[you zou]

Hi again,Sorry, I have one question now, what is the meaning of structure? I 
think coordinates is structure, is it true?If it is true, when I used "editconf 
-f drg.pdb -o drg.gro" number of atoms are different from top file and editconf 
can not add hydrogens to drg.gro. If Gromacs can handle .pdb, How can it do 
this, because number of atoms are different(Which command I have to use?). If 
can't handle it how can I add Hydrogens to drg.gro?Thanks,

you zou wrote:
> Hi again,
> 
> Sorry I confused you with my question. My question is How can I make .gro
> file and .top file from drug.pdb (that removed from drug-enzyme.pdb)?
> 
> If I can use x2top command I will make .top file just, is it true? I think
> .gro file is dependent on forcefiled too so If I use editconf command I will
> miss something, is it true?

If you want to use x2top, the assumption is that the structure is already 
appropriate as is, that is it is properly protonated. The only tool that is 
smart enough to add force field-specific hydrogens is pdb2gmx. If you're using 
OPLS-AA, then you should have all hydrogens present, anyway. If that's true, 
then you can use editconf to create a .gro file (which is not absolutely 
necessary; Gromacs can handle .pdb files just fine). If you don't have all the 
appropriate atoms present in your molecule's structure, then you need to build 
a 
proper structure.

-Justin

> 
> Thank you again
> 
> 
> you zou wrote:
>> Hi Justin,
>> 
>> Thank you for your help, But when I run x2top command there is one error 
>> that is: " Can not find forcefield for atom C1-1 with 2 bonds Can not find
>> forcefield for atom C4-4 with 2 bonds ...
> &g t; Program x2top, VERSION 4.0.5
>> Source code file: x2top.c, line: 207
>> 
>> Fatal error: Could only find a forcefield type for 6 out of 24 atoms"
>> 
> 
> Not all of your atom types are described by ffoplsaa.n2t so you will have to
> add them. There are only a limited number of types that are covered by
> default.
> 
> http://www.gromacs.org/Documentation/File_Formats/.n2t_File
> 
>> I don't know how can I adjust this error. I have one more question again,
>> this command give me a top file, if I want gro file of this pdb (drug that
>> has removed from drug-enzyme complex) how can I do that?
>> 
> 
> Do you just need a .gro file, and not a .top? My understanding from your
> first message was that you needed a topo logy. If you just need a .gro, then
> simply pass your .pdb file to editconf.
> 
> -Justin
> 
>> you zou wrote:
>>> Dear Users,
>>> 
>>> I have one question about Drug-Enzyme Complex,Similar to tutorial If I
>>> 
>> want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
>>> but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
>>> Beta version" server too, or not?
>> 
>> No. You can't use two different force fields in one simulation system.
>> 
>>> If I can't use this server, how can I make .gro file and .itp file for 
>>> drug that remove from initial .pdb file?
>>> 
>> 
>> There are several programs in the User Contributions from the website,
>> x2top (which is distributed with Gromacs), or you can build the topology by
>> hand. No matter what you choose, you ne
> ed a thorough understanding of the mechanics of
>> your chosen force field, methods of validation, and of course Chapter 5 in
>> the
>> 
>> Gromacs manual.
>> 
> 
> 
>  
> Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up
> now. 
> 

-
  
_
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Re: [gmx-users] Re: OPLS-AA/L force field

[Oliver Grant]

*If you are familiar to ambertools (tleap mainly), so you can create your
molecule there, save the amber parameters and use acpype to convert from
amber to gromacs format.

*Thanks Alan, I use tleap and then amb2gmx.pl. It works great, the only
problem is the NAc groups aren't restrained properly so have to manually
edit them in. I'll have to do some reading about acpype...


On 20 May 2010 13:28, Alan  wrote:

> Dear Oliver,
>
>
> On Thu, May 20, 2010 at 13:21,  wrote:
>
>> I'm using GLYCAM06, so it involves a bit more effort to generate a .top
>> and
>> .gro file than just using pdb2gmx but I thought I'd leave it out as I just
>> wanted to explain the method I use to include it. Apologies for the
>> confusion!
>>
>
> If you are familiar to ambertools (tleap mainly), so you can create your
> molecule there, save the amber parameters and use acpype to convert from
> amber to gromacs format.
>
> Alan
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <<
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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[gmx-users] Re: OPLS-AA/L force field

[Alan]

Dear Oliver,

On Thu, May 20, 2010 at 13:21,  wrote:

> I'm using GLYCAM06, so it involves a bit more effort to generate a .top and
> .gro file than just using pdb2gmx but I thought I'd leave it out as I just
> wanted to explain the method I use to include it. Apologies for the
> confusion!
>

If you are familiar to ambertools (tleap mainly), so you can create your
molecule there, save the amber parameters and use acpype to convert from
amber to gromacs format.

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
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Re: [gmx-users] Re: OPLS-AA/L force field

[Oliver Grant]

*I guess that depends on what you mean by "works fine."  *

I mean the method of using pdb2gmx to generate a top and gro and then
appending the gro files and including the .itp files in the .top file, works
if you want to use two force fields. Originally I thought that was the
question.

*I guess it all depends on what you mean (below) by "non amber force field"*

I'm using GLYCAM06, so it involves a bit more effort to generate a .top and
.gro file than just using pdb2gmx but I thought I'd leave it out as I just
wanted to explain the method I use to include it. Apologies for the
confusion!

Oliver



-Justin

On 20 May 2010 13:00, Justin A. Lemkul  wrote:

>
>
> Oliver Grant wrote:
>
>> The force fields have to be compatible but this way works fine.
>>
>>
> I guess that depends on what you mean by "works fine."  If you mean that
> you can produce a stable simulation, then yes, it may "work," but I would
> question the underlying premise of combining different force fields.  If,
> for example, you're using an AMBER force field for, say, a protein, and OPLS
> for a small molecule, then what you're doing is wrong.  The combination
> rules required by both force fields are different, as are the underlying
> derivation schemes and quite possibly some more details I'm not thinking
> about at the moment.
>
> I guess it all depends on what you mean (below) by "non amber force field"
> and how different it is from the actual requirements of the AMBER force
> field you're using.  If this "non amber force field" was designed to be
> compatible with your chosen force field, and there was some suitable
> derivation scheme involved, then things will probably work.  If you're
> mixing and matching parameter sets, be prepared for very tough questions
> from any reviewers who see your work.
>
> -Justin
>
>  On 19 May 2010 12:50, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Oliver Grant wrote:
>>
>>Can you not run pdb2gmx for each of your molecules that you want
>>separate force fields for? Then cat the gro files, renumber and
>>include the molecule types as .itp files in the .top file as
>>below. If I'm doing anything wrong please let me know! :)
>>
>>
>>Combining different force fields into a single system completely
>>invalidates it, so yes, I'd say you're doing something wrong :)
>>
>>-Justin
>>
>>
>> ;
>>;This is your topology file
>>
>>;"What If None Of Your Dreams Come True ?" (E. Costello)
>>;
>>; Include forcefield parameters
>>#include "ffamber99sb.itp"
>>
>>[ atomtypes ]
>>
>>  
>> from
>>the top file of the non amber force field
>>;name  bond_typemasscharge   ptype  sigma
>>   epsilon
>>CYCY  0.  0.  A   3.39967e-01  4.57730e-01
>>O  O  0.  0.  A   2.95992e-01  8.78640e-01
>>HOHO  0.  0.  A   0.0e+00  0.0e+00
>>H1H1  0.  0.  A   2.47135e-01  6.56888e-02
>>O2O2  0.  0.  A   2.95992e-01  8.78640e-01
>>N  N  0.  0.  A   3.25000e-01  7.11280e-01
>>H2H2  0.  0.  A   2.29317e-01  6.56888e-02
>>OYOY  0.  0.  A   3.1e-01  7.11280e-01
>>HCHC  0.  0.  A   2.64953e-01  6.56888e-02
>>H  H  0.  0.  A   1.06908e-01  6.56888e-02
>>C  C  0.  0.  A   3.39967e-01  3.59824e-01
>>OSOS  0.  0.  A   3.1e-01  7.11280e-01
>>CGCG  0.  0.  A   3.39967e-01  4.57730e-01
>>OHOH  0.  0.  A   3.06647e-01  8.80314e-01
>>
>>#include
>>
>>  
>> "protein.itp"from
>>the top file of the amber force field, contains everything
>>usually specified here under [molecule types].
>>
>>; Include Position restraint file
>>#ifdef POSRES
>>#include "posre.itp"
>>#endif
>>
>>#ifdef POSRES_CA
>>#include "CA_posre.itp"
>>#endif
>>
>>#include
>>
>>  
>> "trisacc.itp"from
>>the top file of the non amber force field, contains charges etc.
>>
>>; Include Position restraint file
>>#ifdef POSRES_trisacc
>>#include "trisacc_posre.itp"
>>#endif
>>
>>; Include water topology
>>#include "ffamber_tip3p.itp"
>>
>>#ifdef POSRES_WATER
>>; Position restraint for each water oxygen
>>[ position_restraints ]
>>;  i funct   fcxfcyfcz
>

Re: [gmx-users] Re: OPLS-AA/L force field

[Justin A. Lemkul]

Oliver Grant wrote:

The force fields have to be compatible but this way works fine.



I guess that depends on what you mean by "works fine."  If you mean that you can 
produce a stable simulation, then yes, it may "work," but I would question the 
underlying premise of combining different force fields.  If, for example, you're 
using an AMBER force field for, say, a protein, and OPLS for a small molecule, 
then what you're doing is wrong.  The combination rules required by both force 
fields are different, as are the underlying derivation schemes and quite 
possibly some more details I'm not thinking about at the moment.


I guess it all depends on what you mean (below) by "non amber force field" and 
how different it is from the actual requirements of the AMBER force field you're 
using.  If this "non amber force field" was designed to be compatible with your 
chosen force field, and there was some suitable derivation scheme involved, then 
things will probably work.  If you're mixing and matching parameter sets, be 
prepared for very tough questions from any reviewers who see your work.


-Justin

On 19 May 2010 12:50, Justin A. Lemkul > wrote:




Oliver Grant wrote:

Can you not run pdb2gmx for each of your molecules that you want
separate force fields for? Then cat the gro files, renumber and
include the molecule types as .itp files in the .top file as
below. If I'm doing anything wrong please let me know! :)


Combining different force fields into a single system completely
invalidates it, so yes, I'd say you're doing something wrong :)

-Justin


 ;
;This is your topology file

;"What If None Of Your Dreams Come True ?" (E. Costello)
;
; Include forcefield parameters
#include "ffamber99sb.itp"

[ atomtypes ]

from
the top file of the non amber force field
;name  bond_typemasscharge   ptype  sigma
 epsilon

CYCY  0.  0.  A   3.39967e-01  4.57730e-01
O  O  0.  0.  A   2.95992e-01  8.78640e-01
HOHO  0.  0.  A   0.0e+00  0.0e+00
H1H1  0.  0.  A   2.47135e-01  6.56888e-02
O2O2  0.  0.  A   2.95992e-01  8.78640e-01
N  N  0.  0.  A   3.25000e-01  7.11280e-01
H2H2  0.  0.  A   2.29317e-01  6.56888e-02
OYOY  0.  0.  A   3.1e-01  7.11280e-01
HCHC  0.  0.  A   2.64953e-01  6.56888e-02
H  H  0.  0.  A   1.06908e-01  6.56888e-02
C  C  0.  0.  A   3.39967e-01  3.59824e-01
OSOS  0.  0.  A   3.1e-01  7.11280e-01
CGCG  0.  0.  A   3.39967e-01  4.57730e-01
OHOH  0.  0.  A   3.06647e-01  8.80314e-01

#include

"protein.itp"from
the top file of the amber force field, contains everything
usually specified here under [molecule types].

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

#ifdef POSRES_CA
#include "CA_posre.itp"
#endif

#include

"trisacc.itp"from
the top file of the non amber force field, contains charges etc.

; Include Position restraint file
#ifdef POSRES_trisacc
#include "trisacc_posre.itp"
#endif

; Include water topology
#include "ffamber_tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
  11   1000   1000   1000
#endif

; Include generic topology for ions
#include "Na_amber99sb.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_A   1
trisacc1
SOL 10697
Na  4



2010/5/19 you zou mailto:zou@live.com>
>>


   Hi Justin,

   Thank you for your help, But when I run x2top command there
is one
   error that is:
   "
   Can not find forcefield for atom C1-1 with 2 bonds
   Can not find forcefield for atom C4-4 with 2 bonds
   ...
   Program x2top, VERSION 4.0.5
   Source cod

Re: [gmx-users] Re: OPLS-AA/L force field

[Oliver Grant]

The force fields have to be compatible but this way works fine.

On 19 May 2010 12:50, Justin A. Lemkul  wrote:

>
>
> Oliver Grant wrote:
>
>> Can you not run pdb2gmx for each of your molecules that you want separate
>> force fields for? Then cat the gro files, renumber and include the molecule
>> types as .itp files in the .top file as below. If I'm doing anything wrong
>> please let me know! :)
>>
>
> Combining different force fields into a single system completely
> invalidates it, so yes, I'd say you're doing something wrong :)
>
> -Justin
>
>
>>  ;
>> ;This is your topology file
>>
>> ;"What If None Of Your Dreams Come True ?" (E. Costello)
>> ;
>> ; Include forcefield parameters
>> #include "ffamber99sb.itp"
>>
>> [ atomtypes ]
>> from
>> the top file of the non amber force field
>> ;name  bond_typemasscharge   ptype  sigma  epsilon
>> CYCY  0.  0.  A   3.39967e-01  4.57730e-01
>> O  O  0.  0.  A   2.95992e-01  8.78640e-01
>> HOHO  0.  0.  A   0.0e+00  0.0e+00
>> H1H1  0.  0.  A   2.47135e-01  6.56888e-02
>> O2O2  0.  0.  A   2.95992e-01  8.78640e-01
>> N  N  0.  0.  A   3.25000e-01  7.11280e-01
>> H2H2  0.  0.  A   2.29317e-01  6.56888e-02
>> OYOY  0.  0.  A   3.1e-01  7.11280e-01
>> HCHC  0.  0.  A   2.64953e-01  6.56888e-02
>> H  H  0.  0.  A   1.06908e-01  6.56888e-02
>> C  C  0.  0.  A   3.39967e-01  3.59824e-01
>> OSOS  0.  0.  A   3.1e-01  7.11280e-01
>> CGCG  0.  0.  A   3.39967e-01  4.57730e-01
>> OHOH  0.  0.  A   3.06647e-01  8.80314e-01
>>
>> #include
>> "protein.itp"from
>> the top file of the amber force field, contains everything usually specified
>> here under [molecule types].
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> #ifdef POSRES_CA
>> #include "CA_posre.itp"
>> #endif
>>
>> #include
>> "trisacc.itp"from
>> the top file of the non amber force field, contains charges etc.
>>
>> ; Include Position restraint file
>> #ifdef POSRES_trisacc
>> #include "trisacc_posre.itp"
>> #endif
>>
>> ; Include water topology
>> #include "ffamber_tip3p.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>>   11   1000   1000   1000
>> #endif
>>
>> ; Include generic topology for ions
>> #include "Na_amber99sb.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein_A   1
>> trisacc1
>> SOL 10697
>> Na  4
>>
>>
>>
>> 2010/5/19 you zou mailto:zou@live.com>>
>>
>>
>>Hi Justin,
>>
>>Thank you for your help, But when I run x2top command there is one
>>error that is:
>>"
>>Can not find forcefield for atom C1-1 with 2 bonds
>>Can not find forcefield for atom C4-4 with 2 bonds
>>...
>>Program x2top, VERSION 4.0.5
>>Source code file: x2top.c, line: 207
>>
>>Fatal error:
>>Could only find a forcefield type for 6 out of 24 atoms"
>>
>>I don't know how can I adjust this error.
>>I have one more question again, this command give me a top file, if
>>I want gro file of this pdb (drug that has removed from drug-enzyme
>>complex) how can I do that?
>>
>>you zou wrote:
>>> Dear Users,
>>> > I have one question about Drug-Enzyme Complex,Similar to
>> tutorial If I
>>
>>>
>>  want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
>>   > but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg
>>   > Beta version" server too, or not?
>>
>>No. You can't use two different force fields in one simulation system.
>>
>>
>>
>>> If I can't use this server, how can I make .gro file and .itp file
>> for > drug that remove from initial .pdb file?
>>>
>>There are several programs in the User Contributions from the website,
>> x2top
>>
>>(which is distributed with Gromacs), or you can build the topology by
>> hand. No matter what you choose, you need a thorough understanding of
>> the mechanics of your chosen force field, methods of validation, and of
>> course Chapter 5 in the
>>
>>Gromacs manual.
>>
>>
>>Thanks
>>
>>
>>
>>  
>>Hotmail: Free, trusted and rich email service. Get it now.
>>

Re: [gmx-users] Re: OPLS-AA/L force field

[Justin A. Lemkul]

you zou wrote:

Hi again,

Sorry I confused you with my question. My question is How can I make .gro
file and .top file from drug.pdb (that removed from drug-enzyme.pdb)?

If I can use x2top command I will make .top file just, is it true? I think
.gro file is dependent on forcefiled too so If I use editconf command I will
miss something, is it true?


If you want to use x2top, the assumption is that the structure is already 
appropriate as is, that is it is properly protonated.  The only tool that is 
smart enough to add force field-specific hydrogens is pdb2gmx.  If you're using 
OPLS-AA, then you should have all hydrogens present, anyway.  If that's true, 
then you can use editconf to create a .gro file (which is not absolutely 
necessary; Gromacs can handle .pdb files just fine).  If you don't have all the 
appropriate atoms present in your molecule's structure, then you need to build a 
proper structure.


-Justin



Thank you again


you zou wrote:

Hi Justin,

Thank you for your help, But when I run x2top command there is one error 
that is: " Can not find forcefield for atom C1-1 with 2 bonds Can not find

forcefield for atom C4-4 with 2 bonds ...

&g t; Program x2top, VERSION 4.0.5

Source code file: x2top.c, line: 207

Fatal error: Could only find a forcefield type for 6 out of 24 atoms"



Not all of your atom types are described by ffoplsaa.n2t so you will have to
add them. There are only a limited number of types that are covered by
default.

http://www.gromacs.org/Documentation/File_Formats/.n2t_File


I don't know how can I adjust this error. I have one more question again,
this command give me a top file, if I want gro file of this pdb (drug that
has removed from drug-enzyme complex) how can I do that?



Do you just need a .gro file, and not a .top? My understanding from your
first message was that you needed a topo logy. If you just need a .gro, then
simply pass your .pdb file to editconf.

-Justin


you zou wrote:

Dear Users,

I have one question about Drug-Enzyme Complex,Similar to tutorial If I


want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
Beta version" server too, or not?


No. You can't use two different force fields in one simulation system.

If I can't use this server, how can I make .gro file and .itp file for 
drug that remove from initial .pdb file?




There are several programs in the User Contributions from the website,
x2top (which is distributed with Gromacs), or you can build the topology by
hand. No matter what you choose, you ne

ed a thorough understanding of the mechanics of

your chosen force field, methods of validation, and of course Chapter 5 in
the

Gromacs manual.




 
Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up

now. 



--


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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[gmx-users] Re: OPLS-AA/L force field

[you zou]

Hi again,  Sorry I confused you with my question. My question is How can I make 
.gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I 
can use x2top command I will make .top file just, is it true? I think .gro file 
is dependent on forcefiled too so If I use editconf command I will miss 
something, is it true?Thank you again
you zou wrote:
> Hi Justin,
> 
> Thank you for your help, But when I run x2top command there is one error 
> that is:
> "
> Can not find forcefield for atom C1-1 with 2 bonds
> Can not find forcefield for atom C4-4 with 2 bonds
> ...
> Program x2top, VERSION 4.0.5
> Source code file: x2top.c, line: 207
> 
> Fatal error:
> Could only find a forcefield type for 6 out of 24 atoms"
> 

Not all of your atom types are described by ffoplsaa.n2t so you will have to 
add 
them. There are only a limited number of types that are covered by default.

http://www.gromacs.org/Documentation/File_Formats/.n2t_File

> I don't know how can I adjust this error.
> I have one more question again, this command give me a top file, if I 
> want gro file of this pdb (drug that has removed from drug-enzyme 
> complex) how can I do that?
> 

Do you just need a .gro file, and not a .top? My understanding from your first 
message was that you needed a topology. If you just need a .gro, then simply 
pass your .pdb file to editconf.

-Justin

> you zou wrote:
>> Dear Users,
>> 
>> I have one question about Drug-Enzyme Complex,Similar to tutorial If I 
>>
> want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug 
>> but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
>> Beta version" server too, or not?
> 
> No. You can't use two different force fields in one simulation system.
> 
>> If I can't use this server, how can I make .gro file and .itp file for 
>> drug that remove from initial .pdb file?
>> 
> 
> There are several programs in the User Contributions from the website, x2top 
> (which is distributed with Gromacs), or you can build the topology by hand. 
> No 
> matter what you choose, you need a thorough understanding of the mechanics of 
> your chosen force field, methods of validation, and of course Chapter 5 in 
> the 
> 
> Gromacs manual.
> 

  
_
Hotmail: Trusted email with Microsoft’s powerful SPAM protection.
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Re: [gmx-users] Re: OPLS-AA/L force field

[Justin A. Lemkul]

Oliver Grant wrote:
Can you not run pdb2gmx for each of your molecules that you want 
separate force fields for? Then cat the gro files, renumber and include 
the molecule types as .itp files in the .top file as below. If I'm doing 
anything wrong please let me know! :)


Combining different force fields into a single system completely invalidates it, 
so yes, I'd say you're doing something wrong :)


-Justin



 ;
;This is your topology file
;"What If None Of Your Dreams Come True ?" (E. Costello)
;
; Include forcefield parameters
#include "ffamber99sb.itp"

[ atomtypes ] 
from 
the top file of the non amber force field

;name  bond_typemasscharge   ptype  sigma  epsilon
CYCY  0.  0.  A   3.39967e-01  4.57730e-01
O  O  0.  0.  A   2.95992e-01  8.78640e-01
HOHO  0.  0.  A   0.0e+00  0.0e+00
H1H1  0.  0.  A   2.47135e-01  6.56888e-02
O2O2  0.  0.  A   2.95992e-01  8.78640e-01
N  N  0.  0.  A   3.25000e-01  7.11280e-01
H2H2  0.  0.  A   2.29317e-01  6.56888e-02
OYOY  0.  0.  A   3.1e-01  7.11280e-01
HCHC  0.  0.  A   2.64953e-01  6.56888e-02
H  H  0.  0.  A   1.06908e-01  6.56888e-02
C  C  0.  0.  A   3.39967e-01  3.59824e-01
OSOS  0.  0.  A   3.1e-01  7.11280e-01
CGCG  0.  0.  A   3.39967e-01  4.57730e-01
OHOH  0.  0.  A   3.06647e-01  8.80314e-01

#include 
"protein.itp"from 
the top file of the amber force field, contains everything usually 
specified here under [molecule types].


; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

#ifdef POSRES_CA
#include "CA_posre.itp"
#endif

#include 
"trisacc.itp"from 
the top file of the non amber force field, contains charges etc.


; Include Position restraint file
#ifdef POSRES_trisacc
#include "trisacc_posre.itp"
#endif

; Include water topology
#include "ffamber_tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
#include "Na_amber99sb.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_A   1
trisacc1
SOL 10697
Na  4



2010/5/19 you zou mailto:zou@live.com>>

Hi Justin,

Thank you for your help, But when I run x2top command there is one
error that is:
"
Can not find forcefield for atom C1-1 with 2 bonds
Can not find forcefield for atom C4-4 with 2 bonds
...
Program x2top, VERSION 4.0.5
Source code file: x2top.c, line: 207

Fatal error:
Could only find a forcefield type for 6 out of 24 atoms"

I don't know how can I adjust this error.
I have one more question again, this command give me a top file, if
I want gro file of this pdb (drug that has removed from drug-enzyme
complex) how can I do that?

you zou wrote:
> Dear Users,
> 
> I have one question about Drug-Enzyme Complex,Similar to tutorial If I 



>
  want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug 
> but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
> Beta version" server too, or not?


No. You can't use two different force fields in one simulation system.



> If I can't use this server, how can I make .gro file and .itp file for 
> drug that remove from initial .pdb file?
> 

There are several programs in the User Contributions from the website, x2top 



(which is distributed with Gromacs), or you can build the topology by hand. No 
matter what you choose, you need a thorough understanding of the mechanics of 
your chosen force field, methods of validation, and of course Chapter 5 in the 



Gromacs manual.


Thanks



Hotmail: Free, trusted and rich email service. Get it now.


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Please search the archive at http://www.gromacs.org/search before
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Re: [gmx-users] Re: OPLS-AA/L force field

[Oliver Grant]

Can you not run pdb2gmx for each of your molecules that you want separate
force fields for? Then cat the gro files, renumber and include the molecule
types as .itp files in the .top file as below. If I'm doing anything wrong
please let me know! :)

 ;
;This is your topology file
;"What If None Of Your Dreams Come True ?" (E. Costello)
;
; Include forcefield parameters
#include "ffamber99sb.itp"

[ atomtypes ]
from
the top file of the non amber force field
;name  bond_typemasscharge   ptype  sigma  epsilon
CYCY  0.  0.  A   3.39967e-01  4.57730e-01
O  O  0.  0.  A   2.95992e-01  8.78640e-01
HOHO  0.  0.  A   0.0e+00  0.0e+00
H1H1  0.  0.  A   2.47135e-01  6.56888e-02
O2O2  0.  0.  A   2.95992e-01  8.78640e-01
N  N  0.  0.  A   3.25000e-01  7.11280e-01
H2H2  0.  0.  A   2.29317e-01  6.56888e-02
OYOY  0.  0.  A   3.1e-01  7.11280e-01
HCHC  0.  0.  A   2.64953e-01  6.56888e-02
H  H  0.  0.  A   1.06908e-01  6.56888e-02
C  C  0.  0.  A   3.39967e-01  3.59824e-01
OSOS  0.  0.  A   3.1e-01  7.11280e-01
CGCG  0.  0.  A   3.39967e-01  4.57730e-01
OHOH  0.  0.  A   3.06647e-01  8.80314e-01

#include
"protein.itp"from
the top file of the amber force field, contains everything usually specified
here under [molecule types].

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

#ifdef POSRES_CA
#include "CA_posre.itp"
#endif

#include
"trisacc.itp"from
the top file of the non amber force field, contains charges etc.

; Include Position restraint file
#ifdef POSRES_trisacc
#include "trisacc_posre.itp"
#endif

; Include water topology
#include "ffamber_tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
#include "Na_amber99sb.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_A   1
trisacc1
SOL 10697
Na  4



2010/5/19 you zou 

>  Hi Justin,
>
> Thank you for your help, But when I run x2top command there is one error
> that is:
> "
> Can not find forcefield for atom C1-1 with 2 bonds
> Can not find forcefield for atom C4-4 with 2 bonds
> ...
> Program x2top, VERSION 4.0.5
> Source code file: x2top.c, line: 207
>
> Fatal error:
> Could only find a forcefield type for 6 out of 24 atoms"
>
> I don't know how can I adjust this error.
> I have one more question again, this command give me a top file, if I want
> gro file of this pdb (drug that has removed from drug-enzyme complex) how
> can I do that?
>
> you zou wrote:
> > Dear Users,
> >
> > I have one question about Drug-Enzyme Complex,Similar to tutorial If I
>
> >
>   want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
> > but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg
> > Beta version" server too, or not?
>
> No. You can't use two different force fields in one simulation system.
>
> > If I can't use this server, how can I make .gro file and .itp file for
> > drug that remove from initial .pdb file?
> >
>
> There are several programs in the User Contributions from the website, x2top
>
> (which is distributed with Gromacs), or you can build the topology by hand. No
> matter what you choose, you need a thorough understanding of the mechanics of
> your chosen force field, methods of validation, and of course Chapter 5 in the
>
> Gromacs manual.
>
>
> Thanks
>
>
> --
> Hotmail: Free, trusted and rich email service. Get it 
> now.
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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Re: [gmx-users] Re: OPLS-AA/L force field

[Justin A. Lemkul]

you zou wrote:

Hi Justin,

Thank you for your help, But when I run x2top command there is one error 
that is:

"
Can not find forcefield for atom C1-1 with 2 bonds
Can not find forcefield for atom C4-4 with 2 bonds
...
Program x2top, VERSION 4.0.5
Source code file: x2top.c, line: 207

Fatal error:
Could only find a forcefield type for 6 out of 24 atoms"



Not all of your atom types are described by ffoplsaa.n2t so you will have to add 
them.  There are only a limited number of types that are covered by default.


http://www.gromacs.org/Documentation/File_Formats/.n2t_File


I don't know how can I adjust this error.
I have one more question again, this command give me a top file, if I 
want gro file of this pdb (drug that has removed from drug-enzyme 
complex) how can I do that?




Do you just need a .gro file, and not a .top?  My understanding from your first 
message was that you needed a topology.  If you just need a .gro, then simply 
pass your .pdb file to editconf.


-Justin


you zou wrote:

Dear Users,

I have one question about Drug-Enzyme Complex,Similar to tutorial If I 

  want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug 
but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
Beta version" server too, or not?


No. You can't use two different force fields in one simulation system.

If I can't use this server, how can I make .gro file and .itp file for 
drug that remove from initial .pdb file?




There are several programs in the User Contributions from the website, x2top 
(which is distributed with Gromacs), or you can build the topology by hand. No 
matter what you choose, you need a thorough understanding of the mechanics of 
your chosen force field, methods of validation, and of course Chapter 5 in the 


Gromacs manual.


Thanks



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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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[gmx-users] Re: OPLS-AA/L force field

[you zou]

Hi Justin,
Thank you for your help, But when I run x2top command there is one error that 
is:"Can not find forcefield for atom C1-1 with 2 bondsCan not find forcefield 
for atom C4-4 with 2 bonds...Program x2top, VERSION 4.0.5Source code file: 
x2top.c, line: 207Fatal error:Could only find a forcefield type for 6 out of 24 
atoms"I don't know how can I adjust this error.I have one more question again, 
this command give me a top file, if I want gro file of this pdb (drug that has 
removed from drug-enzyme complex) how can I do that?
you zou wrote:
> Dear Users,
> 
> I have one question about Drug-Enzyme Complex,Similar to tutorial If I 
> want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug 
> but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
> Beta version" server too, or not?

No. You can't use two different force fields in one simulation system.

> If I can't use this server, how can I make .gro file and .itp file for 
> drug that remove from initial .pdb file?
> 

There are several programs in the User Contributions from the website, x2top 
(which is distributed with Gromacs), or you can build the topology by hand. No 
matter what you choose, you need a thorough understanding of the mechanics of 
your chosen force field, methods of validation, and of course Chapter 5 in the 
Gromacs manual.

Thanks

  
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[gmx-users] Re: OPLS-AA/L force field

[Alan]

Hi You Zou,

Complementing Justin's message, I would invite you to take a look at
acpype.googlecode.com. It's my attempt to address problems like yours.
There's also links to some options besides ACPYPE.

Bear in mind that you should know what you're doing. I would suggest you to
read the Wiki's there as well as several references also indicated there.
ACPYPE is far from being perfect but it can be very helpful. I have my own
methodology where it would require using RED Server for accurate partial
charge calculations (ACPYPE may use SQM, which is semi-empirical, via
Antechamber), then ACPYPE (which is mostly designed for Amber FF) and then
MKTOP for getting the oplsaa atom types.

Feel free to contact.

Best regards,

Alan

On Tue, May 18, 2010 at 01:28,  wrote:

> Message: 2
> Date: Mon, 17 May 2010 12:58:09 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] OPLS-AA/L force field
> To: Discussion list for GROMACS users 
> Message-ID: <4bf175a1.9040...@vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> you zou wrote:
> > Dear Users,
> >
> > I have one question about Drug-Enzyme Complex,Similar to tutorial If I
> > want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
> > but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg
> > Beta version" server too, or not?
>
> No.  You can't use two different force fields in one simulation system.
>
> > If I can't use this server, how can I make .gro file and .itp file for
> > drug that remove from initial .pdb file?
> >
>
> There are several programs in the User Contributions from the website,
> x2top
> (which is distributed with Gromacs), or you can build the topology by hand.
>  No
> matter what you choose, you need a thorough understanding of the mechanics
> of
> your chosen force field, methods of validation, and of course Chapter 5 in
> the
> Gromacs manual.
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> -Justin
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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