[gmx-users] Structure factor and scattering intensity in gromacs 5.1.4

[Rakesh Pant]

Dear All,

How to calculate structure factor and scattering intensity in gromacs
5.1.4.

Thanks,
Rakesh



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Re: [gmx-users] request

[Rakesh Pant]

What is -s md ? in the command line.

On 05-Dec-2017 12:32 AM,  wrote:

hi.what causes this error?

Command line:
gmx mdrun -s md -cpi md_0_1_prev.cpt

Output file appending has been requested,
but some output files listed in the checkpoint file md_0_1_prev.cpt
are not present or not named as the output files by the current program:
Expect output files present:

Expected output files not present or named differently:
md_0_1.log
md_0_1.xtc
md_0_1.edr

---
Program: gmx mdrun, version 2016.3
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)

Fatal error:
File appending requested, but 3 of the 3 output files are not present or
are
named differently. For safety reasons, GROMACS-2016 and later only
allows file
appending to be used when all files have the same names as they had in
the
original run. Checkpointing is merely intended for plain continuation of
runs.
For safety reasons you must specify all file names (e.g. with -deffnm),
and
all these files must match the names used in the run prior to
checkpointing
since we will append to them by default. If the files are not available,
you
can add the -noappend flag to mdrun and write separate new parts. For
mere
concatenation of files, you should use the gmx trjcat tool instead.
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Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

[Rakesh Pant]

Dear Alex,

But g-x2top doesn't work till we define all atom types in .n2t file.

Thanks


On 26-Nov-2017 9:34 PM, "Alexandr Nasedkin"  wrote:

Hi,

You will need to have both ffbonded.itp and ffnonbonded.itp .

atomname2type.n2t is needed for g_x2top to make it work correctly.

Good luck.


-Alex



On 26/11/2017 10:52, Rakesh Pant wrote:

> Dear,  Alex
> Does it mean, we do not need to define all the atomtypes in the .nt2 file.
> It is enough to define all types in bonded and non-bonded itp.
>
> Thanks,
> Rakesh
>
>
>
> <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature&lang=en&refer
> ral=rakesh.p...@students.iiserpune.ac.in&idSignature=22>
>
> On Sun, Nov 26, 2017 at 3:27 PM, Alexandr Nasedkin 
> wrote:
>
> Edit the content of you ffnonbonded.itp file approximately this way:
>>
>> [ atomtypes ]
>> ;nameat.nummasschargeptypesigma epsilon
>> C1412.001.08A0.440000.63  ;
>> OCE815.999400-0.70A0.354000.159705  ; C-O-C
>> Bridging Oxygen;
>> OCH815.999400-0.51A0.354000.159705  ; C-O-H
>> Oxygen;
>>
>> HCO1 1.0080000.32A0.044900.235725  ; H-O-C
>> Hydrogen;
>> 
>>
>> You would need to search literature for respective ff parameters: all the
>> above parameters are taken from another topology to give a template.
>>
>>
>> -Alex
>>
>>
>> On 26/11/2017 10:37, Rakesh Pant wrote:
>>
>> Dear Alex,
>>>If I use O atoms to define the respective functional groups, then how
>>> to
>>> include the C atoms present in the molecule.
>>>
>>> Thanks,
>>> Rakesh
>>>
>>>
>>>
>>> <https://mailtrack.io/> Sent with Mailtrack
>>> <https://mailtrack.io/install?source=signature&lang=en&refer
>>> ral=rakesh.p...@students.iiserpune.ac.in&idSignature=22>
>>>
>>> On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin >> >
>>> wrote:
>>>
>>> Hi,
>>>
>>>> As I understood the problem, you need to distinguish between surface and
>>>> buried carbons?
>>>>
>>>> You could define two atomtypes that differ in name and use it to process
>>>> with x2top.
>>>>
>>>> Below is an example of *.n2t lines. You would need to change the charges
>>>> and bondlengthes.
>>>>
>>>> ...
>>>>
>>>> OOCH-1.0515.99942C0.154 H 0.1; oxygen, -OH
>>>> group
>>>> OOCE-1.0515.99942C0.154 C 0.154; bridge
>>>> oxygen
>>>>
>>>> ...
>>>>
>>>> Then you need *.n2t file in your ff.
>>>>
>>>> Good luck!
>>>>
>>>>
>>>> -Alex
>>>>
>>>>
>>>> On 25/11/2017 22:06, Justin Lemkul wrote:
>>>>
>>>>
>>>> On 11/25/17 3:31 PM, Rakesh Pant wrote:
>>>>>
>>>>> But then I how will include the C atom (which is also one of the
>>>>>
>>>>>> atomtypes)?
>>>>>>
>>>>>> No idea, but I know people on this list have dealt with graphene oxide
>>>>>>
>>>>> before, so hopefully someone else chimes in.
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>> --
>>>>>
>>>> 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
>>>>
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>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>
>>>>
>>>>
>>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
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>>
>
>
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Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

[Rakesh Pant]

Dear,  Alex
Does it mean, we do not need to define all the atomtypes in the .nt2 file.
It is enough to define all types in bonded and non-bonded itp.

Thanks,
Rakesh



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On Sun, Nov 26, 2017 at 3:27 PM, Alexandr Nasedkin 
wrote:

> Edit the content of you ffnonbonded.itp file approximately this way:
>
> [ atomtypes ]
> ;nameat.nummasschargeptypesigma epsilon
> C1412.001.08A0.440000.63  ;
> OCE815.999400-0.70A0.354000.159705  ; C-O-C
> Bridging Oxygen;
> OCH815.999400-0.51A0.354000.159705  ; C-O-H
> Oxygen;
>
> HCO1 1.0080000.32A0.044900.235725  ; H-O-C
> Hydrogen;
> 
>
> You would need to search literature for respective ff parameters: all the
> above parameters are taken from another topology to give a template.
>
>
> -Alex
>
>
> On 26/11/2017 10:37, Rakesh Pant wrote:
>
>> Dear Alex,
>>   If I use O atoms to define the respective functional groups, then how to
>> include the C atoms present in the molecule.
>>
>> Thanks,
>> Rakesh
>>
>>
>>
>> <https://mailtrack.io/> Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature&lang=en&refer
>> ral=rakesh.p...@students.iiserpune.ac.in&idSignature=22>
>>
>> On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin 
>> wrote:
>>
>> Hi,
>>>
>>> As I understood the problem, you need to distinguish between surface and
>>> buried carbons?
>>>
>>> You could define two atomtypes that differ in name and use it to process
>>> with x2top.
>>>
>>> Below is an example of *.n2t lines. You would need to change the charges
>>> and bondlengthes.
>>>
>>> ...
>>>
>>> OOCH    -1.0515.99942C0.154 H 0.1; oxygen, -OH
>>> group
>>> OOCE-1.0515.99942C0.154 C 0.154; bridge
>>> oxygen
>>>
>>> ...
>>>
>>> Then you need *.n2t file in your ff.
>>>
>>> Good luck!
>>>
>>>
>>> -Alex
>>>
>>>
>>> On 25/11/2017 22:06, Justin Lemkul wrote:
>>>
>>>
>>>> On 11/25/17 3:31 PM, Rakesh Pant wrote:
>>>>
>>>> But then I how will include the C atom (which is also one of the
>>>>> atomtypes)?
>>>>>
>>>>> No idea, but I know people on this list have dealt with graphene oxide
>>>> before, so hopefully someone else chimes in.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> --
>>> 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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>>>
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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>
>>
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>



-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm
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Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

[Rakesh Pant]

Dear Alex,
 If I use O atoms to define the respective functional groups, then how to
include the C atoms present in the molecule.

Thanks,
Rakesh



<https://mailtrack.io/> Sent with Mailtrack
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On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin 
wrote:

> Hi,
>
> As I understood the problem, you need to distinguish between surface and
> buried carbons?
>
> You could define two atomtypes that differ in name and use it to process
> with x2top.
>
> Below is an example of *.n2t lines. You would need to change the charges
> and bondlengthes.
>
> ...
>
> OOCH-1.0515.99942C0.154 H 0.1; oxygen, -OH
> group
> OOCE-1.0515.99942C0.154 C 0.154; bridge oxygen
>
> ...
>
> Then you need *.n2t file in your ff.
>
> Good luck!
>
>
> -Alex
>
>
> On 25/11/2017 22:06, Justin Lemkul wrote:
>
>>
>>
>> On 11/25/17 3:31 PM, Rakesh Pant wrote:
>>
>>> But then I how will include the C atom (which is also one of the
>>> atomtypes)?
>>>
>>
>> No idea, but I know people on this list have dealt with graphene oxide
>> before, so hopefully someone else chimes in.
>>
>> -Justin
>>
>>
> --
> 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
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm
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Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

[Rakesh Pant]

But then I how will include the C atom (which is also one of the atomtypes)?

Thanks,




<https://mailtrack.io/> Sent with Mailtrack
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On Sun, Nov 26, 2017 at 1:56 AM, Justin Lemkul  wrote:

>
>
> On 11/25/17 3:21 PM, Rakesh Pant wrote:
>
>> Dear Justin,
>>
>> I am trying to use it for graphene oxide (layer), then what would be a
>> better way if not g_x2top.
>>
>
> Epoxide O and phenolic O have different connectivity (two C vs. one C and
> one H), so write the .n2t entries first based on O rather than C.
>
> -Justin
>
> Thanks,
>>
>>
>>
>> <https://mailtrack.io/> Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature&lang=en&refer
>> ral=rakesh.p...@students.iiserpune.ac.in&idSignature=22>
>>
>>
>> On Sun, Nov 26, 2017 at 1:48 AM, Justin Lemkul  wrote:
>>
>>
>>> On 11/25/17 3:12 PM, Rakesh Pant wrote:
>>>
>>> Dear All,
>>>>
>>>> How does the utility g_x2top works?
>>>> If we have similar connectivity in a molecule, then how will it read
>>>> different atom types. Suppose a C atom is connected to 4 bonds (3 carbon
>>>> atoms and 1 O atom, say in epoxy group) and similarly another C atom is
>>>> also connected to 4 atoms (3 C atoms and 1 O atom, but the different
>>>> functional group, e.g phenolic group). Both are present in the same
>>>> molecule, then how should we define both in the .n2t file so that
>>>> g_x2top
>>>> reads both the atomtypes.
>>>>
>>>> The only difference in that case might be bond lengths, though they may
>>> not be different enough to be distinguished (they would have to differ by
>>> at least 10% to be outside of the default tolerance). x2top is not a
>>> particularly smart program, and whatever it matches first will be what it
>>> writes to the topology. If you have some very complex molecule, this may
>>> not be a useful tool.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> 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.
>>>
>>>
>>
>>
> --
> ======
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> 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
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm
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Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

[Rakesh Pant]

Dear Justin,

I am trying to use it for graphene oxide (layer), then what would be a
better way if not g_x2top.

Thanks,



<https://mailtrack.io/> Sent with Mailtrack
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On Sun, Nov 26, 2017 at 1:48 AM, Justin Lemkul  wrote:

>
>
> On 11/25/17 3:12 PM, Rakesh Pant wrote:
>
>> Dear All,
>>
>> How does the utility g_x2top works?
>> If we have similar connectivity in a molecule, then how will it read
>> different atom types. Suppose a C atom is connected to 4 bonds (3 carbon
>> atoms and 1 O atom, say in epoxy group) and similarly another C atom is
>> also connected to 4 atoms (3 C atoms and 1 O atom, but the different
>> functional group, e.g phenolic group). Both are present in the same
>> molecule, then how should we define both in the .n2t file so that g_x2top
>> reads both the atomtypes.
>>
>
> The only difference in that case might be bond lengths, though they may
> not be different enough to be distinguished (they would have to differ by
> at least 10% to be outside of the default tolerance). x2top is not a
> particularly smart program, and whatever it matches first will be what it
> writes to the topology. If you have some very complex molecule, this may
> not be a useful tool.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> 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.
>



-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm
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[gmx-users] Regarding use of g_x2top utility in Gromacs

[Rakesh Pant]

Dear All,

How does the utility g_x2top works?
If we have similar connectivity in a molecule, then how will it read
different atom types. Suppose a C atom is connected to 4 bonds (3 carbon
atoms and 1 O atom, say in epoxy group) and similarly another C atom is
also connected to 4 atoms (3 C atoms and 1 O atom, but the different
functional group, e.g phenolic group). Both are present in the same
molecule, then how should we define both in the .n2t file so that g_x2top
reads both the atomtypes.

Thanks,
Rakesh

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[gmx-users] Doubt from Graphene oxide layer

[Rakesh Pant]

Hi,

I want to create a Graphene Oxide (GO) layer using some computational
tools. It consists of different type of functional groups like hydroxy,
carboxylic, and epoxy. VMD can generate Graphene layer. How Can I generate
GO layer by using some computational tools?

Thanks

-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm
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Re: [gmx-users] Doubt from force constant calculations

[Rakesh Pant]

Dear Justin,

Could you briefly tell how the vibrational analysis is done. Which method
and software is generally used.

Thanks
Rakesh

On Fri, Mar 17, 2017 at 7:16 PM, Justin Lemkul  wrote:

>
>
> On 3/17/17 7:53 AM, Rakesh Pant wrote:
>
>> Dear all,
>>
>> How to calculate force constant for bonds and angles using quantum
>> chemistry calculations.
>>
>>
> Typically a vibrational analysis is done and force constants are set to
> reproduce the frequencies.
>
> -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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>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm
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[gmx-users] Doubt from force constant calculations

[Rakesh Pant]

Dear all,

How to calculate force constant for bonds and angles using quantum
chemistry calculations.


Thanks
Rakesh
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Re: [gmx-users] Doubt from topology creation

[Rakesh Pant]

Dear Justin

I am sharing the link, please have a look.

https://www.dropbox.com/s/b1czeuf9hbrjwxi/atomname2type.n2t?dl=0
https://www.dropbox.com/s/b8mfxktucuqge5k/file.pdb?dl=0
https://www.dropbox.com/s/7v58inob81ogo3m/to.top?dl=0

Thanks




On Tue, Feb 21, 2017 at 11:30 PM, Justin Lemkul  wrote:

>
>
> On 2/21/17 10:05 AM, Rakesh Pant wrote:
>
>> Dear all,
>>
>> I am trying to create a topology for a molecule using g_x2top and have
>> defined all the atoms with connectivity in *atomname.n2t* file with
>> different opls no. for all different types of atoms.
>>
>> But when I create topology, it does not identify all different atomtypes
>> and takes one common opls no. for some of the atoms.
>>
>> I have attached the pdb file and .n2t file.
>>
>>
> The list does not accept attachments.  If you want to share files, upload
> them to a file-sharing service and provide the URL.
>
> -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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm
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[gmx-users] Doubt from topology creation

[Rakesh Pant]

Dear all,

I am trying to create a topology for a molecule using g_x2top and have
defined all the atoms with connectivity in *atomname.n2t* file with
different opls no. for all different types of atoms.

But when I create topology, it does not identify all different atomtypes
and takes one common opls no. for some of the atoms.

I have attached the pdb file and .n2t file.

Thanks

-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm
-- 
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[gmx-users] Doubt from topology creation using g_x2top

[Rakesh Pant]

Dear all,

I am trying to create a topology for a molecule using g_x2top and have
defined all the atoms with connectivity in *atomname.n2t* file with
different opls no. for all different types of atoms.

But when I create topology, it does not identify all different atomtypes
and takes one common opls no. for some of the atoms.

Thanks


Rakesh
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