[gmx-users] gromacs.org_gmx-users Digest, Vol 163, Issue 116

Tue Nov 28 07:49:08 CET 2017

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> Today's Topics:
>
>    1. Pdb2gmx melts molecules due to bad distances (GIANMARCO BARTALINI)
>    2. Not enough memory. Failed to realloc (RAHUL SURESH)
>    3. Re: pH dependent simulation (Justin Lemkul)
>    4. Re: pH dependent simulation (Justin Lemkul)
>    5. Re: Pdb files generated on Lincs warning (Justin Lemkul)
>    6. Re: Fatal error in grompp (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 27 Nov 2017 12:04:04 +0100
> From: GIANMARCO BARTALINI <gianmarco.bartali at student.unisi.it>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Pdb2gmx melts molecules due to bad distances
> Message-ID:
> 	<CAO_Bx_=O6RdgHhbkMr2_AWCsZoOihkfk-qvJAOZ0BEN-Us=bgA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello guys, I produced a system "protein + lipid membrane" using the
> online
> tool CHARMM-GUI. Since I need to use the Amber force field, I added the
> Lipids17 force field inside Gromacs. The implementation should work fine,
> since the conversion of an equilibrated structure produces a nice and
> correct gro file. But when I try to convert the (not minimized) PDB file
> that I get from CHARMM-GUI using pdb2gmx, I get a gro structure where many
> lipid molecules are melted together (due to their bad distances). If I use
> this structure for a minimization, the calculation stops due to bad
> energies. Do you know how to solve this issue?
> Thank you in advance,
>
> Gianmarco
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 27 Nov 2017 17:47:36 +0530
> From: RAHUL SURESH <drrahulsuresh at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Not enough memory. Failed to realloc
> Message-ID:
> 	<CAAtfiTsVMh7YBzpADaZ1gqwCy=PSptD=jkAT-K076Stwfp0CBg at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Users
>
> I am trying to carryout protein-metal interaction using charmm36 ff.
> During
> solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
> solv.gro"
> *i receive a error stating
>
>
>
>
>
>
>
>
> *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for
> atoms_->atom,atoms_->atom=0(called from
> file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/topology/atomsbuilder.cpp,line
> 86)". *
> I have enough space to carry out this simulation and I am using 2016
> version of gromacs.
>
> I couldnt diagonise the error exactly. Any help on this will be of great
> use.
>
> Thank you
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 27 Nov 2017 08:31:18 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] pH dependent simulation
> Message-ID: <fd27208f-d447-aeea-1ac4-bfad6090327b at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Thank you so much sir.
>
> On 11/26/17 11:09 PM, zaved at tezu.ernet.in wrote:
>> Hello Everyone
>>
>> I am trying to simulate a protein at two pH (7.4 and 9.0) using
>> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
>> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
>> positively charged residues.
>>
>> However upon predicting the pKa values using H++ server, I am getting
>> the
>> same pKa values for all the charged residues (at pH 7.4 and pH 9). And
>> the
>> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
>> should have different pKa values at pH 7 and 9).
>
> Why do you expect that? There are no amino acids with pKa in that range,
> so nothing should change unless there are unique microenvironments that
> shift canonical pKa values. As H++ has not detected any, likely your
> protein behaves canonically. You can confirm your calculated pKa values
> with another method, like PROPKA, to be sure.
>
> -Justin
>
>> Whether I am in the right direction or doing something wrong!!!
>>
>> Can anyone kindly suggest me how to proceed further?
>>
>> Any suggestion is appreciated.
>>
>> Thank You
>> Zaved
>>
>>
>> * * * D I S C L A I M E R * * *
>> This e-mail may contain privileged information and is intended solely
>> for the individual named. If you are not the named addressee you should
>> not disseminate, distribute or copy this e-mail. Please notify the
>> sender immediately by e-mail if you have received this e-mail in error
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>> corrupted, lost, destroyed, delayed, or may contain viruses. The
>> recipient must verify the integrity of this e-mail message.
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 27 Nov 2017 08:32:42 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] pH dependent simulation
> Message-ID: <ac236610-f41c-1830-3903-3a98ce7d459d at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/27/17 1:02 AM, Tasneem Kausar wrote:
>> pKa of amino acid residue is a constant quantity. Depending on the pH
>> you
>
> That's not strictly true. Titratable amino acids can be found in unique
> microenvironments that cause shifts in canonical values. For instance,
> there are some catalytic lysines known in hydrophobic environments that
> have pKa values of ~4 instead of the canonical value of ~10.5.
>
> -Justin
>
>> can protonate and deprotonate amino acid according to the pKa of
>> particular
>> residue.
>>
>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
>> Virus-free.
>> www.avast.com
>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>> On Mon, Nov 27, 2017 at 9:39 AM, <zaved at tezu.ernet.in> wrote:
>>
>>> Hello Everyone
>>>
>>> I am trying to simulate a protein at two pH (7.4 and 9.0) using
>>> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
>>> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
>>> positively charged residues.
>>>
>>> However upon predicting the pKa values using H++ server, I am getting
>>> the
>>> same pKa values for all the charged residues (at pH 7.4 and pH 9). And
>>> the
>>> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
>>> should have different pKa values at pH 7 and 9).
>>>
>>> Whether I am in the right direction or doing something wrong!!!
>>>
>>> Can anyone kindly suggest me how to proceed further?
>>>
>>> Any suggestion is appreciated.
>>>
>>> Thank You
>>> Zaved
>>>
>>>
>>> * * * D I S C L A I M E R * * *
>>> This e-mail may contain privileged information and is intended solely
>>> for
>>> the individual named. If you are not the named addressee you should not
>>> disseminate, distribute or copy this e-mail. Please notify the sender
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>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
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>>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 27 Nov 2017 08:33:29 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Pdb files generated on Lincs warning
> Message-ID: <b79f6257-5fc1-352e-4333-ba77b3297e9d at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/27/17 1:04 AM, atb files wrote:
>>
>>
>>
>>              Dear Users,When there is a Lincs warning (sometimes because
>> of exceeding warnangle etc) the gromacs generates pdb
>> files. My questions is:What is purpose of generating pdb
>> files? What information they give? Which information we
>> need to look for to analyse those pdbs.?ThanksYogi?Sent
>> using Zoho Mail
>>
>
> These are the coordinates before and after applying constraints for each
> domain of the system. They are not PBC-corrected so they can be really
> hard to interpret. mdrun prints which atoms are having issues, which is
> usually sufficient to begin diagnosing what is going on.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 27 Nov 2017 08:35:07 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Fatal error in grompp
> Message-ID: <1ff29b4a-a512-3a6c-4094-157c07e5fc34 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/27/17 5:25 AM, Saumyak Mukherjee wrote:
>> Dear All,
>>
>> I want to calculate the interaction energy between water and protein
>> backbone. However, in mdp file, when I am using
>>
>> energygrps = SOL backbone
>>
>> ?grompp is returning the following error.
>>
>> Fatal error:
>> atoms 1 and 2 in charge group 1 of molecule type 'Protein_chain_A' are
>> in
>> different energy groups
>>
>> Can someone kindly point out my mistake??
>
> You can't make the backbone a separate energy group. Look at what atoms
> 1 and 2 are - likely it's the N-terminal N and one H atom, which have to
> be in the same group to do a group-based, pairwise energy decomposition.
> Whatever groups you establish have to contain full charge groups.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at 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
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> End of gromacs.org_gmx-users Digest, Vol 163, Issue 116
> *******************************************************
>

* * * D I S C L A I M E R * * *
This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message.