[gmx-users] Re: question about dihedral angle in *.itp file
linfu
linfu3200 at 126.com
Mon Jan 8 06:46:26 CET 2007
Thank you very much for your answer!
I have check manual in chapter4. I am still confused about this sentence.
As we know, each dihedral was counted only once(?) in the program. however,
if several torsional dihedral angles with different parameters can be defined
on the same set of atoms i, j, k, and l, does this mean that this dihedral will
be counted several times.
for second question about multiplicity m
i am really confused about the physical mean of m, according to equation
V=k(1+Col(delta)*Cos(m*phi))
it seems that m is just the periodiocity of Cosine function.
Could anyone help me figure out, Thank you very much:)
BEST REGARDS
Fu Lin
======= 2007-01-03 19:00:05 您在来信中写道：=======
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>Today's Topics:
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> 1. Re: Error when adding a unnatural amio acid (David van der Spoel)
> 2. Re: question about dihedral angle in *.itp file
> (David van der Spoel)
> 3. (no subject) (sharada)
> 4. Re: (no subject) (Mark Abraham)
> 5. Re: (no subject) (Caterina Arcangeli)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 03 Jan 2007 08:50:37 +0100
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] Error when adding a unnatural amio acid
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <459B604D.7030209 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>yuemin liu wrote:
>> Hi, Everyone,
>>
>> I got Error when adding a unnatural amio acid in a
>> protein. I have all the rtp and hdb file modified
>> using information either from ffgmx.rtp ffgmx.hdb or
>> thr rtp file form progdrg. There is no H1 in either
>> rtp file or my new pdb file. When I try use pdb2gmx to
>> generate top file, it always give the error message
>> following;
>> "Atom H1 not found in rtp database in residue ASO, it
>> looks a bit like H". I know it refers to the Hydrogen
>> of the peptide bond which has nothing wrong there.
>>
>> Hope can get help from you with this,
>>
>And by the way, avoid using ffgmx. Search archives for reasons why.
>
>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: 46 18 471 4205 fax: 46 18 511 755
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>------------------------------
>
>Message: 2
>Date: Wed, 03 Jan 2007 08:51:47 +0100
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] question about dihedral angle in *.itp file
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <459B6093.9000005 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=GB2312
>
>linfu wrote:
>> Dear GMX community!
>>
>> I have a question about dihedral angle in *.itp file.
>> question 1:
>>
>> why several torsional dihedral angles with different parameters can be defined
>> on the same set of atoms i, j, k, and l.
>
>why not?
>
>>
>> question 2:
>>
>> how do we get multiplicity m if we want to make some parameter for some torsional
>> angle.
>
>which functional form? check equations in chapter 4.
>
>
>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: 46 18 471 4205 fax: 46 18 511 755
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>------------------------------
>
>Message: 3
>Date: Wed, 3 Jan 2007 13:31:44 +0530 (IST)
>From: sharada <sharada at ccmb.res.in>
>Subject: [gmx-users] (no subject)
>To: gmx-users at gromacs.org
>Message-ID: <3588128.1167811304121.JavaMail.root at mailserver>
>Content-Type: text/plain; charset="us-ascii"
>
>Hello gmx_users,
>I wish you a very happy and prosperous new year 2007. I have a very fundamental question in trjcat usage. I have two *.trr files of 5ns and 10 ns runs . I would like to concanate the two and make a 15ns trr file. How to give the command so that the starting time of the 10ns file should be 5001ps and not 0ps and end time is 15000ps and not 10000 ps. May this is a trivial question. Kindly help. I have tried using the following command :
>trjcat -f nchnp3_5npep.trr nchnp3_10pep.trr -settime -o nchnp3_15pep.trr -b 0.00 -e 15000
>its taking 0ps to 10000ps only
>hoping for help
>regards
>sharada
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>------------------------------
>
>Message: 4
>Date: Wed, 03 Jan 2007 19:46:06 +1100
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Subject: Re: [gmx-users] (no subject)
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <459B6D4E.8030005 at anu.edu.au>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>sharada wrote:
>> Hello gmx_users,
>>
>> I wish you a very happy and prosperous new year 2007. I have a very
>> fundamental question in trjcat usage. I have two *.trr files of 5ns and
>> 10 ns runs . I would like to concanate the two and make a 15ns trr
>> file. How to give the command so that the starting time of the 10ns file
>> should be 5001ps and not 0ps and end time is 15000ps and not 10000 ps.
>> May this is a trivial question. Kindly help. I have tried using the
>> following command :
>> trjcat -f nchnp3_5npep.trr nchnp3_10pep.trr -settime -o nchnp3_15pep.trr
>> -b 0.00 -e 15000
>
>It's just like the command line utility cat... it will do a straight
>concatenation.
>
>trjcat -f 5n.trr 10n.trr -o 15n.trr
>
>should do what you want.
>
>Check using gmxdump , of course
>
>Mark
>
>
>------------------------------
>
>Message: 5
>Date: Wed, 03 Jan 2007 10:11:45 +0100
>From: Caterina Arcangeli <caterina.arcangeli at casaccia.enea.it>
>Subject: Re: [gmx-users] (no subject)
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <459B7351.1020803 at casaccia.enea.it>
>Content-Type: text/plain; charset=ISO-8859-1
>
>
>Hi,
>using the command:
>trjcat -f nchnp3_5npep.trr nchnp3_10pep.trr -o nchnp3_15pep.trr -settime
>
>the program will ask you the start time of each file. Try putting "5001"
>for the first file and "c" (continue) for the second file.
>It should be work.
>
>Ciao
>Caterina
>
>
>
>Mark Abraham wrote:
>> sharada wrote:
>>> Hello gmx_users,
>>>
>>> I wish you a very happy and prosperous new year 2007. I have a very
>>> fundamental question in trjcat usage. I have two *.trr files of 5ns
>>> and 10 ns runs . I would like to concanate the two and make a 15ns
>>> trr file. How to give the command so that the starting time of the
>>> 10ns file should be 5001ps and not 0ps and end time is 15000ps and not
>>> 10000 ps. May this is a trivial question. Kindly help. I have tried
>>> using the following command :
>>> trjcat -f nchnp3_5npep.trr nchnp3_10pep.trr -settime -o
>>> nchnp3_15pep.trr -b 0.00 -e 15000
>>
>> It's just like the command line utility cat... it will do a straight
>> concatenation.
>>
>> trjcat -f 5n.trr 10n.trr -o 15n.trr
>>
>> should do what you want.
>>
>> Check using gmxdump , of course
>>
>> Mark
>> _______________________________________________
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>
>
>--
>Caterina Arcangeli
>ENEA, Computing and Modelling Unit (CAMO)
>Casaccia Research Center - Post Bag 026
>Via Anguillarese 301 - 00060 Roma
>phone +39 06.3048.6898
>fax +39 06.3048.6860
>http://www.enea.it
>
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致
礼！
linfu
linfu3200 at 126.com
2007-01-08
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