[gmx-users] Re:gmx-users Digest, Vol 113, Issue 108

[aixintiankong]

Dear prof.
      The format of  parameters is convenient to the  software of Amber and not to gromacs. if i use the parameters i must use some tools to convert it to  the itp format for gromacs. so i use acpype to get itp format.
     i just doubt that i use amber99sb for protein and AM1-BBC for ligand and resp charge for cofactor.  it looks like unprofessional and i don't know whether can affect the the MD . I do like this is right or not ?







At 2013-09-24 18:00:04,gmx-users-request at gromacs.org wrote:
>Send gmx-users mailing list submissions to
>	gmx-users at gromacs.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	http://lists.gromacs.org/mailman/listinfo/gmx-users
>or, via email, send a message with subject or body 'help' to
>	gmx-users-request at gromacs.org
>
>You can reach the person managing the list at
>	gmx-users-owner at gromacs.org
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of gmx-users digest..."
>
>
>Today's Topics:
>
>   1. Re: Re: Charmm 36 forcefield with verlet cut-off scheme
>      (Justin Lemkul)
>   2. Re: The charge of cofactor and ligand (Justin Lemkul)
>   3. Re: Fatal Error: Residue 'DMP' not found in residue topology
>      database (Santhosh Kumar Nagarajan)
>   4. Re: Regarding g_sgangle index file (Venkat Reddy)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Mon, 23 Sep 2013 21:25:19 -0400
>From: Justin Lemkul <jalemkul at vt.edu>
>Subject: Re: [gmx-users] Re: Charmm 36 forcefield with verlet cut-off
>	scheme
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <5240E9FF.1020200 at vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>On 9/23/13 4:04 PM, akk5r wrote:
>> With what was said: what do you all think of the following parameters for
>> Charmm 36:
>>
>> rlist = 1.2
>> rlistlong = 1.4
>> vdwtype = cutoff
>> rvdw-switch = 1.0
>> rvdw = 1.2
>> rcouloumb = 1.2
>> vdw-modifier = Potential-shift-Verlet
>> DispCorr = No
>> cutoff-scheme = Verlet
>>
>
>rvdw-switch has no effect here, and I have no real hard evidence to know whether 
>or not this will produce the same effect as the traditional settings.  You would 
>have to carefully demonstrate that what you're doing doesn't break the force field.
>
>-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
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>==================================================
>
>
>------------------------------
>
>Message: 2
>Date: Mon, 23 Sep 2013 21:26:15 -0400
>From: Justin Lemkul <jalemkul at vt.edu>
>Subject: Re: [gmx-users] The charge of cofactor and ligand
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <5240EA37.4090903 at vt.edu>
>Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
>On 9/23/13 5:10 PM, aixintiankong wrote:
>> Dear,
>> First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and a ligand. when i check  the charge of NAD+, I find that the distribution of charge is not correct, the N1N atom should be positive charge but the chimera give a negative. so i copy the resp charge form http://www.pharmacy.manchester.ac.uk/bryce/amber  and then replace the AM1-BCC with the resp charge form    http://www.pharmacy.manchester.ac.uk/bryce/amber  . At last, i use "acpype –i ben.mol2 –c user" to get the nad.itp file.
>>          so the NAD+ use the RESP charge and the ligand use the   AM1-BCC charges , can i do like this ?
>>          i use this method to get the NAD+.itp file? is correct or not ?
>>
>>
>
>Why not just use the parameters that are already published?  Unless there's 
>something wrong with them, there's no need to reinvent the wheel.
>
>-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
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>==================================================
>
>
>------------------------------
>
>Message: 3
>Date: Mon, 23 Sep 2013 20:43:28 -0700 (PDT)
>From: Santhosh Kumar Nagarajan <santhoshrajan90 at gmail.com>
>Subject: [gmx-users] Re: Fatal Error: Residue 'DMP' not found in
>	residue topology database
>To: gmx-users at gromacs.org
>Message-ID: <1379994208045-5011420.post at n6.nabble.com>
>Content-Type: text/plain; charset=us-ascii
>
>Justin..
>I understand the problem..
>But.. How to generate a .rtp file myself..
>
>
>-----
>Santhosh Kumar Nagarajan
>MTech Bioinformatics
>SRM University
>Chennai
>India
>--
>View this message in context: http://gromacs.5086.x6.nabble.com/Fatal-Error-Residue-DMP-not-found-in-residue-topology-database-tp5011333p5011420.html
>Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
>------------------------------
>
>Message: 4
>Date: Tue, 24 Sep 2013 11:09:20 +0530
>From: Venkat Reddy <venkat4bt at gmail.com>
>Subject: Re: [gmx-users] Regarding g_sgangle index file
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID:
>	<CAFhLg7WGw9qd_tKusLA=VZr-Aj-N55MMamGomLp3kUHEpcYJ6Q at mail.gmail.com>
>Content-Type: text/plain; charset=ISO-8859-1
>
>Hello Sir,
>I have been using the new tool "gmx gangle". My actual intention is to
>calculate the orientation between any two same molecules (say cholesterol)
>throughout the trajectory and there are 40 cholesterol molecules. But I
>couldn't calculate it. I am getting "0" as output. My command is:
>gmx gangle -f traj_noPBC.xtc -s topol.tpr -n -g1 vector -g2 vector -group1
>'resname CHOL and name R5 R0' -group2 'resname CHOL and name R5 R0' -oav
>-oall -oh
>
>
>On Mon, Sep 23, 2013 at 11:19 PM, Teemu Murtola <teemu.murtola at gmail.com>wrote:
>
>> Hi,
>>
>> On Thu, Sep 19, 2013 at 7:19 PM, Venkat Reddy <venkat4bt at gmail.com> wrote:
>>
>> > @Teemu Murtola: Are there any modifications to the other gmx tools? (eg:
>> > rdf calculation with dynamic selection...etc). I am trying to explore the
>> > new version.
>> >
>>
>> Unfortunately, there are currently very few tools using the new mechanisms.
>> http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 lists
>> most of the changes: in practice, there's 'gmx distance' as a more flexible
>> alternative to computing distances, and g_select (now 'gmx select') has
>> gotten a few extra output options. There's also at least one new tool, 'gmx
>> freevolume'.
>>
>> Best regards,
>> Teemu
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
>-- 
>With Best Wishes
>Venkat Reddy Chirasani
>PhD student
>Laboratory of Computational Biophysics
>Department of Biotechnology
>IIT Madras
>Chennai
>INDIA-600036
>
>
>------------------------------
>
>-- 
>gmx-users mailing list
>gmx-users at gromacs.org
>http://lists.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>
>End of gmx-users Digest, Vol 113, Issue 108
>*******************************************