subject:"\[gmx\-users\] topology"

Re: 答复: [gmx-users] topology file of ligand

2013-10-15 Thread Justin Lemkul




On 10/15/13 12:25 PM, sunyeping wrote:

Thank you Dr. Lemkul,

Could you recommand some primary literatures which are most usefule for me to 
understand the force field?



The ones cited in the Gromacs manual are a good start.  One should never attempt 
to use a force field without scrutinizing its history, assumptions, and 
parametrization methods...


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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答复: [gmx-users] topology file of ligand

2013-10-15 Thread sunyeping

Thank you Dr. Lemkul,
 
Could you recommand some primary literatures which are most usefule for me to 
understand the force field? 

Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

--发件人：Justin 
Lemkul 发送时间：2013年10月16日(星期三) 00:05收件人：gromacs 
主　题：Re: [gmx-users] topology file of ligandOn 10/15/13 
11:24 AM, sunyeping wrote:> Dear gromacs users,>> I am study the tutorial for 
protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with 
JZ4). The tutorial use PRODRG to produce the topology file. The author state 
that he immediately notice three things that are wrong with this topology, 
which include charge group, H atom charge, etc.> And the author then 
reconstructed a topology file. I don't understand how the charge group and 
charge of individual atom are correctly assigned. Could you explain it to 
me?>The Gromos96 parameter sets assign charges and charge groups based on 
chemical functional groups that are transferable between molecules. Spotting 
inaccuracies and knowing how to fix them come with understanding how the force 
field was derived (read the primary literature and study existing 
molecules).-Justin-- ==Justin 
A. Lemkul, Ph.D.Postdoctoral FellowDepartment of Pharmaceutical SciencesSchool 
of PharmacyHealth Sciences Facility II, Room 601University of Maryland, 
Baltimore20 Penn St.Baltimore, MD 21201jalem...@outerbanks.umaryland.edu | 
(410) 706-7441==-- gmx-users 
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Re: [gmx-users] topology file of ligand

2013-10-15 Thread Justin Lemkul




On 10/15/13 11:24 AM, sunyeping wrote:

Dear gromacs users,

I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: 
T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the 
topology file. The author state that he  immediately notice three things that 
are wrong with this topology, which include charge group, H atom charge, etc.
  And the author then reconstructed a topology file.  I don't understand 
how the charge group and charge of individual atom are correctly assigned. 
Could you explain it to me?



The Gromos96 parameter sets assign charges and charge groups based on chemical 
functional groups that are transferable between molecules.  Spotting 
inaccuracies and knowing how to fix them come with understanding how the force 
field was derived (read the primary literature and study existing molecules).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] topology file of ligand

2013-10-15 Thread sunyeping

Dear gromacs users,
 
I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: 
T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the 
topology file. The author state that he  immediately notice three things that 
are wrong with this topology, which include charge group, H atom charge, etc. 
     And the author then reconstructed a topology file.  I don't understand how 
the charge group and charge of individual atom are correctly assigned. Could 
you explain it to me? 
 
Thanks.
 
Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

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Re: [gmx-users] topology and coordinate file not matching after grompp

2013-07-31 Thread Justin Lemkul




On 7/31/13 6:04 AM, chinnu657 wrote:

Hello,

I have a problem and although I've read almost everything the internet could
offer on how differently people have approached this problem, mine hasn't
been solved yet.

Basically, I am trying to mix 2 different proteins in one box and after
doing my grompp to neutralise the system, I get the error number of
coordinates in coordinate file (solvated.gro, 85059) does not match topology
(topol.top, 85079).

This is how my topology file looks:
;GROMACS toplogy

;
;Include the force field
#include "oplsaa.ff/forcefield.itp"


; Include chain topologies
#include "topol_1AKI.itp"
#include "topol_2CDS.itp"

;Include water topology
#include "spce.itp"

;Include generic ion topology
#include "ions.itp"

[ system ]
Two proteins in water

[ molecules ]
Protein_1AKI1
Protein_2CDS1
SOL 27053

How can I deduce from this data that the number of coordinates in topol.top
is 85079. And what exactly should I do to reduce the number of molecules
here so that the 2 files have the same number of coordinates.



Number of atoms in Protein_1AKI [moleculetype] + number of atoms in Protein_2CDS 
[moleculetype] + (3*27053) is the number of atoms that the topology specifies. 
Cross-check that against the coordinate file.  This error always arises for the 
same reason - incorrect bookkeeping of some sort.  You haven't said how you 
built the system or what commands you gave, for instance, to genbox, so it's 
hard to be more specific.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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[gmx-users] topology and coordinate file not matching after grompp

2013-07-31 Thread chinnu657

Hello,

I have a problem and although I've read almost everything the internet could
offer on how differently people have approached this problem, mine hasn't
been solved yet.

Basically, I am trying to mix 2 different proteins in one box and after
doing my grompp to neutralise the system, I get the error number of
coordinates in coordinate file (solvated.gro, 85059) does not match topology
(topol.top, 85079).

This is how my topology file looks:
;GROMACS toplogy

;
;Include the force field
#include "oplsaa.ff/forcefield.itp"

; Include chain topologies
#include "topol_1AKI.itp"
#include "topol_2CDS.itp"

;Include water topology
#include "spce.itp"

;Include generic ion topology
#include "ions.itp"

[ system ]
Two proteins in water

[ molecules ]
Protein_1AKI1
Protein_2CDS1
SOL 27053

How can I deduce from this data that the number of coordinates in topol.top
is 85079. And what exactly should I do to reduce the number of molecules
here so that the 2 files have the same number of coordinates.

I will really appreciate the help. I am pretty new with MD simulations

Kind Regards,
Chinnu

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