Re: [AMBER] AMBER Digest, Vol 1932, Issue 1

From: Elvis Martis <elvis.martis.bcp.edu.in> Date: Tue, 23 May 2017 08:27:02 +0000

--
*Regards*
Garima Singh
AcSIR-PhD Fellow
Biotechnology Division
CSIR-CIMAP
Lucknow
garimabioinfo.gmail.com
*INDIA* Please don't print this e-mail unless you really need to. Be Green !
On Sat, May 13, 2017 at 12:30 AM, <amber-request.ambermd.org> wrote:
> Send AMBER mailing list submissions to
>         amber.ambermd.org
>
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> or, via email, send a message with subject or body 'help' to
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
>    1. Re: <Na 1> Could not find vdW (or other) parameters for type:
>       Na (David A Case)
>    2. Re: <Na 1> Could not find vdW (or other) parameters for type:
>       Na (Thakur, Abhishek)
>    3. Re: Tip3p water box size for two different systems.
>       (Elvis  Martis)
>    4. Fwd: Problem in splitting mdcrd file with cpptraj
>       (Manjula Saravanan)
>    5. Re: Tip3p water box size for two different systems.
>       (Saman Yousuf ali)
>    6. Re: Tip3p water box size for two different systems.
>       (Elvis  Martis)
>    7. Re: Tip3p water box size for two different systems. (Bill Ross)
>    8. How to use Amber in HPC (Garima Singh)
>    9. Re: How to use Amber in HPC (Elvis  Martis)
>   10. Re: <Na 1> Could not find vdW (or other) parameters for type:
>       Na (David A Case)
>   11. EEL and VDW Notification on minimization with sander/pmemd
>       (Charles Mariasoosai)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 11 May 2017 15:02:00 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] <Na 1> Could not find vdW (or other) parameters
>         for type: Na
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20170511190200.spq3psgfgfqql6fj.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Thu, May 11, 2017, Thakur, Abhishek wrote:
> >
> >
> > I have two sodium and one chlorine ions positioned at a specific
> > position in my complex structure.
> >
> > So for this complex when I am trying to make prmtop and inpcrd file I am
> > getting an error for my sodium ions.
> >
> >
> > For atom: .R<Na 600>.A<Na 1> Could not find vdW (or other) parameters
> > for type: Na
>
> You should tell us what commands you gave to tleap, that is, which
> parameters
> (usually via leaprc files) you loaded.
>
> However, the correct atom and residue name for sodium ions is "NA" (for
> both
> the atom and the residue).  This is the PDB standard, which we try to
> follow.  For backwards compatibility, I think tleap still recognizes "Na+",
> but that is an Amber-ism and should be discouraged.
>
> The correct atom/residue name for chloride is "CL".  There is not enough
> information in your email to determine how that is being processed.  You
> can always use the "desc" command in tleap to see what residues are loaded.
>
> ....hope this helps....dac
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 11 May 2017 21:37:54 +0000
> From: "Thakur, Abhishek" <axt651.miami.edu>
> Subject: Re: [AMBER] <Na 1> Could not find vdW (or other) parameters
>         for type: Na
> To: AMBER Mailing List <amber.ambermd.org>, "david.case.rutgers.edu"
>         <david.case.rutgers.edu>
> Message-ID:
>         <MWHPR07MB2814EC37B7BD9F42125481F09EED0.MWHPR07MB2814.namprd
> 07.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Dr. Case,
>
>
> I have been doing
>
> tleap -s -f leaprc.ff14SB.ORIG
> source leaprc.gaff
> loadamberparams UNK.frcmod
> loadoff UNK.lib
> Na = loadmol2 Na.mol2
> Cl = loadmol2 Cl.mol2
> R_config = loadpdb C8_2.pdb
> solvateBox R_config TIP3PBOX 10
> charge R_config
> addIons R_config Cl- 2
> loadAmberParams frcmod.ionsjc_tip3p
> saveamberparm R_config C8.prmtop C8.inpcrd
> savepdb R_config complex.pdb
> quit
>
>
> ________________________________
> From: David A Case <david.case.rutgers.edu>
> Sent: Thursday, May 11, 2017 8:02:00 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for
> type: Na
>
> On Thu, May 11, 2017, Thakur, Abhishek wrote:
> >
> >
> > I have two sodium and one chlorine ions positioned at a specific
> > position in my complex structure.
> >
> > So for this complex when I am trying to make prmtop and inpcrd file I am
> > getting an error for my sodium ions.
> >
> >
> > For atom: .R<Na 600>.A<Na 1> Could not find vdW (or other) parameters
> > for type: Na
>
> You should tell us what commands you gave to tleap, that is, which
> parameters
> (usually via leaprc files) you loaded.
>
> However, the correct atom and residue name for sodium ions is "NA" (for
> both
> the atom and the residue).  This is the PDB standard, which we try to
> follow.  For backwards compatibility, I think tleap still recognizes "Na+",
> but that is an Amber-ism and should be discouraged.
>
> The correct atom/residue name for chloride is "CL".  There is not enough
> information in your email to determine how that is being processed.  You
> can always use the "desc" command in tleap to see what residues are loaded.
>
> ....hope this helps....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.am
> bermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_
> IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=nKxpXK4_KFVej2ezr8KcHwKSq
> r8tIcHT_B3HB1orZtA&s=5YMX75rqQOg5Rs2aVAT-Xr6iJsP0XKQoqXDxhjj3x3Y&e=
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 12 May 2017 05:18:59 +0000
> From: "Elvis  Martis" <elvis.martis.bcp.edu.in>
> Subject: Re: [AMBER] Tip3p water box size for two different systems.
> To: Saman Yousuf ali <saman.yousufali64.yahoo.com>, AMBER Mailing List
>         <amber.ambermd.org>
> Message-ID:
>         <MAXPR01MB0218C03DD70632714822818CA3E20.MAXPR01MB0218.INDPRD
> 01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> Since the proteins will be bigger, the box size will automatically be
> bigger if you use solvation shell method (using buffer).
> However, I don't see a need why you must keep the box size same.
>
> ? ? Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> ?at?Bombay College of Pharmacy
>
>
> A??Kalina, Santacruz [E], Mumbai 400098, INDIA
> W?www.elvismartis.in
> Skype.?adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Saman Yousuf ali [mailto:saman.yousufali64.yahoo.com]
> Sent: Thursday, May 11, 2017 8:27 PM
> To: amber.ambermd.org
> Subject: [AMBER] Tip3p water box size for two different systems.
>
> Dear All,
> I am interested to simulate complex protein system in dimeric and
> monomeric form separately. Residues in case of monomeric system is 1-268
> including one Ligand and cofactor. Dimeric system is double in size. My
> question is for solvation of each systems tip3p water size should be same
> for both? or dimeric system box size must be bigger in size as compared to
> monomer?
>
> Thanks
>
>
>
>
> ?
> ?
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> ------------------------------
>
> Message: 4
> Date: Fri, 12 May 2017 10:50:31 +0530
> From: Manjula Saravanan <manjusimba.gmail.com>
> Subject: [AMBER] Fwd: Problem in splitting mdcrd file with cpptraj
> To: amber.ambermd.org
> Message-ID:
>         <CANtcf8AmC6dK0EaN9zMWhvZV8UZ-s_dKL9Nf_3YW62eZsDq26g.mail.gm
> ail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> *With Best Regards*
> *S. Manjula*
> *Research Scholar*
> *Laboratory of Biocrystallography and Computational Molecular Biology*
> *Department of Physics*
> *Periyar University*
> *Salem-11*
> *Tamilnadu*
>
>
>
> Dear Sir/Madam,
>                 I am trying to split my mdcrd file which contains 1580
> frames. I want only 50 frames starting from 1159-1209 for the normal mode
> calculation. my input file is,
>
> t
>
>
> *rajin prod3.mdcrd 1159 1209 1 trajout prod30ns_50frames1.mdcrd*
> But it shows some error in the output as follows,
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Error: start 1159 > #Frames (141), no frames will be processed.Error:
> Could not set up input trajectory 'prod3.mdcrd'.    1 errors encountered
> reading input.CPPTRAJ: Trajectory Analysis. V14.25    ___  ___  ___
> ___     | \/ | \/ | \/ |     _|_/\_|_/\_|_/\_|_    Reading
> 'com_solv.prmtop' as Amber TopologyINPUT: Reading Input from file
> cpptraj.in <http://cpptraj.in>  [trajin prod3.mdcrd 1159 1209 50 ]
> Reading 'prod3.mdcrd' as Amber TrajectoryTIME: Total execution time: 0.3070
> seconds.*
>
> Kindly help me to solve this problem.
>
> *With Best Regards*
> *S. Manjula*
> *Research Scholar*
> *Laboratory of Biocrystallography and Computational Molecular Biology*
> *Department of Physics*
> *Periyar University*
> *Salem-11*
> *Tamilnadu*
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 12 May 2017 05:30:43 +0000 (UTC)
> From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
> Subject: Re: [AMBER] Tip3p water box size for two different systems.
> To: Elvis Martis <elvis.martis.bcp.edu.in>,     AMBER Mailing List
>         <amber.ambermd.org>
> Message-ID: <212545802.10940389.1494567043539.mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Martis,Thanks for response. I do not want to use same box size, I
> understand that as system size increase water box size should be bigger.? I
> am just asking about box size idea for my system. like if I generate 8
> angstrom tip3p box around my monomeric system then what is the ideal box
> size for dimer? I hope you get my point.
>
> Thanks
> ?
>
>
>     On Friday, May 12, 2017 10:19 AM, Elvis Martis <
> elvis.martis.bcp.edu.in> wrote:
>
>
>  Hi,
> Since the proteins will be bigger, the box size will automatically be
> bigger if you use solvation shell method (using buffer).
> However, I don't see a need why you must keep the box size same.
>
> ? ? Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> ?at?Bombay College of Pharmacy
>
>
> A??Kalina, Santacruz [E], Mumbai 400098, INDIA
> W?www.elvismartis.in
> Skype.?adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Saman Yousuf ali [mailto:saman.yousufali64.yahoo.com]
> Sent: Thursday, May 11, 2017 8:27 PM
> To: amber.ambermd.org
> Subject: [AMBER] Tip3p water box size for two different systems.
>
> Dear All,
> I am interested to simulate complex protein system in dimeric and
> monomeric form separately. Residues in case of monomeric system is 1-268
> including one Ligand and cofactor. Dimeric system is double in size. My
> question is for solvation of each systems tip3p water size should be same
> for both? or dimeric system box size must be bigger in size as compared to
> monomer?
>
> Thanks
>
>
>
>
> ?
> ?
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 12 May 2017 05:42:34 +0000
> From: "Elvis  Martis" <elvis.martis.bcp.edu.in>
> Subject: Re: [AMBER] Tip3p water box size for two different systems.
> To: Saman Yousuf ali <saman.yousufali64.yahoo.com>, AMBER Mailing List
>         <amber.ambermd.org>
> Message-ID:
>         <MAXPR01MB0218A4C8C7BCF1375A8349BFA3E20.MAXPR01MB0218.INDPRD
> 01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> There is nothing idea here.
> You can use 8 angstrom buffer for both your dimer and your monomer and
> there should be no problem.
>
>     Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
>  at Bombay College of Pharmacy
>
>
>
> A  Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
>
> Skype. adrian_elvis12<https://webapp.wisestamp.com/>
>
>
>
>
>
> From: Saman Yousuf ali [mailto:saman.yousufali64.yahoo.com]
> Sent: Friday, May 12, 2017 11:01 AM
> To: Elvis Martis <elvis.martis.bcp.edu.in>; AMBER Mailing List <
> amber.ambermd.org>
> Subject: Re: [AMBER] Tip3p water box size for two different systems.
>
> Dear Martis,
> Thanks for response. I do not want to use same box size, I understand that
> as system size increase water box size should be bigger.  I am just asking
> about box size idea for my system. like if I generate 8 angstrom tip3p box
> around my monomeric system then what is the ideal box size for dimer? I
> hope you get my point.
>
> Thanks
>
>
>
> On Friday, May 12, 2017 10:19 AM, Elvis Martis <elvis.martis.bcp.edu.in
> <mailto:elvis.martis.bcp.edu.in>> wrote:
>
> Hi,
> Since the proteins will be bigger, the box size will automatically be
> bigger if you use solvation shell method (using buffer).
> However, I don't see a need why you must keep the box size same.
>
>     Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
>  at Bombay College of Pharmacy
>
>
> A  Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<http://www.elvismartis.in>
> Skype. adrian_elvis12
>
>
>
> -----Original Message-----
> From: Saman Yousuf ali [mailto:saman.yousufali64.yahoo.com<mailto:
> saman.yousufali64.yahoo.com>]
> Sent: Thursday, May 11, 2017 8:27 PM
> To: amber.ambermd.org<mailto:amber.ambermd.org>
> Subject: [AMBER] Tip3p water box size for two different systems.
>
> Dear All,
> I am interested to simulate complex protein system in dimeric and
> monomeric form separately. Residues in case of monomeric system is 1-268
> including one Ligand and cofactor. Dimeric system is double in size. My
> question is for solvation of each systems tip3p water size should be same
> for both? or dimeric system box size must be bigger in size as compared to
> monomer?
>
> Thanks
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 11 May 2017 22:52:06 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] Tip3p water box size for two different systems.
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <f8a144e0-0ff7-599e-a903-ca92b990136b.cgl.ucsf.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> 8 Angstroms seems small in both cases. I would consider 10, since the
> system will shrink on equilibration, as inititial vdw voids go away.
>
> Bil;
>
>
> On 5/11/17 10:42 PM, Elvis Martis wrote:
> > Hi,
> > There is nothing idea here.
> > You can use 8 angstrom buffer for both your dimer and your monomer and
> there should be no problem.
> >
> >      Best Regards
> >
> >
> >
> > Elvis Martis
> > Ph.D. Student (Computational Chemistry)
> >   at Bombay College of Pharmacy
> >
> >
> >
> > A  Kalina, Santacruz [E], Mumbai 400098, INDIA
> > W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> >
> > Skype. adrian_elvis12<https://webapp.wisestamp.com/>
> >
> >
> >
> >
> >
> > From: Saman Yousuf ali [mailto:saman.yousufali64.yahoo.com]
> > Sent: Friday, May 12, 2017 11:01 AM
> > To: Elvis Martis <elvis.martis.bcp.edu.in>; AMBER Mailing List <
> amber.ambermd.org>
> > Subject: Re: [AMBER] Tip3p water box size for two different systems.
> >
> > Dear Martis,
> > Thanks for response. I do not want to use same box size, I understand
> that as system size increase water box size should be bigger.  I am just
> asking about box size idea for my system. like if I generate 8 angstrom
> tip3p box around my monomeric system then what is the ideal box size for
> dimer? I hope you get my point.
> >
> > Thanks
> >
> >
> >
> > On Friday, May 12, 2017 10:19 AM, Elvis Martis <elvis.martis.bcp.edu.in
> <mailto:elvis.martis.bcp.edu.in>> wrote:
> >
> > Hi,
> > Since the proteins will be bigger, the box size will automatically be
> bigger if you use solvation shell method (using buffer).
> > However, I don't see a need why you must keep the box size same.
> >
> >      Best Regards
> >
> >
> >
> > Elvis Martis
> > Ph.D. Student (Computational Chemistry)
> >   at Bombay College of Pharmacy
> >
> >
> > A  Kalina, Santacruz [E], Mumbai 400098, INDIA
> > W www.elvismartis.in<http://www.elvismartis.in>
> > Skype. adrian_elvis12
> >
> >
> >
> > -----Original Message-----
> > From: Saman Yousuf ali [mailto:saman.yousufali64.yahoo.com<mailto:
> saman.yousufali64.yahoo.com>]
> > Sent: Thursday, May 11, 2017 8:27 PM
> > To: amber.ambermd.org<mailto:amber.ambermd.org>
> > Subject: [AMBER] Tip3p water box size for two different systems.
> >
> > Dear All,
> > I am interested to simulate complex protein system in dimeric and
> monomeric form separately. Residues in case of monomeric system is 1-268
> including one Ligand and cofactor. Dimeric system is double in size. My
> question is for solvation of each systems tip3p water size should be same
> for both? or dimeric system box size must be bigger in size as compared to
> monomer?
> >
> > Thanks
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Fri, 12 May 2017 16:23:49 +0530
> From: Garima Singh <garimabioinfo.gmail.com>
> Subject: [AMBER] How to use Amber in HPC
> To: amber.ambermd.org
> Message-ID:
>         <CAD=mwY1K1a0GkNUpTekGnmM2NQ1WtEfOqjf5uYE2Lt+ZaZWt6g.mail.gm
> ail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Amber users,
>
>
> I am using AMBER 14 in my system having processor* Intel? Xeon(R) CPU
> E5-1607 v3 . 3.10GHz* *? 4* . It takes a lot time to calculating the
> output.I want to run my  Amber MD calculation in HPC. How to perform MD
> calculation using AMBER 14 in HPC .Which script file i need?
>
>  Kindly provide your valuable suggestion
>
> Thanks
> *Regards*
> Garima Singh
> AcSIR-PhD Fellow
> Central Institute Of Medicinal And Aromatic Plant
> CSIR-CIMAP
> Lucknow
> garimabioinfo.gmail.com
>
>
>
>
> *INDIA* Please don't print this e-mail unless you really need to. Be Green
> !
>
>
> ------------------------------
>
> Message: 9
> Date: Fri, 12 May 2017 11:40:31 +0000
> From: "Elvis  Martis" <elvis.martis.bcp.edu.in>
> Subject: Re: [AMBER] How to use Amber in HPC
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
>         <MAXPR01MB0218ACE31AD2FAAF62ECFDF5A3E20.MAXPR01MB0218.INDPRD
> 01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="utf-8"
>
> Hi
> You will need a pbs or torque script to submit any kind of jobs on the HPC.
> The best would be to consult the system admin for the HPC
> A typical pbs script will look like this, you must edit it to suit your
> system and your needs
>
> #!/bin/bash
> #PBS -l nodes=2, ppn=2
> #PBS -l walltime=50:00:00
> #PBS -j oe
> #PBS -q normal
> #PBS -N <JOB NAME>
> #PBS -l pmem=2048MB
> #PBS -l vmem=2048MB
>  cat $PBS_NODEFILE
> cd <WORK DIRECTORY>
>
> set mpich_run =  "XYZ/ mpirun"  >>> consult system admin
> set sander.MPI (pmemd.MPI) = "$AMBERHOME/bin/sander.MPI(or pmemd.MPI)"  >>
> pointer for sander(or pmemd)
> $mpich_run -machinefile $PBS_NODEFILE -np `wc -l < $PBS_NODEFILE`
> $mpich_run -np $NSLOTS $sander.MPI (or $pmemd.MPI) -O -i INFILE -c
> INPUT_CORDINATE -o outfile -r output_coordinate -x trajectory_file   >>>
> sander command will remain same
>
>
> ? ? Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> ?at?Bombay College of Pharmacy
>
>
> A??Kalina, Santacruz [E], Mumbai 400098, INDIA
> W?www.elvismartis.in
> Skype.?adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Garima Singh [mailto:garimabioinfo.gmail.com]
> Sent: Friday, May 12, 2017 4:24 PM
> To: amber.ambermd.org
> Subject: [AMBER] How to use Amber in HPC
>
> Dear Amber users,
>
>
> I am using AMBER 14 in my system having processor* Intel? Xeon(R) CPU
> E5-1607 v3 . 3.10GHz* *? 4* . It takes a lot time to calculating the
> output.I want to run my  Amber MD calculation in HPC. How to perform MD
> calculation using AMBER 14 in HPC .Which script file i need?
>
>  Kindly provide your valuable suggestion
>
> Thanks
> *Regards*
> Garima Singh
> AcSIR-PhD Fellow
> Central Institute Of Medicinal And Aromatic Plant CSIR-CIMAP Lucknow
> garimabioinfo.gmail.com
>
>
>
>
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>
> Message: 10
> Date: Fri, 12 May 2017 08:33:34 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] <Na 1> Could not find vdW (or other) parameters
>         for type: Na
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20170512123334.s45ul3lt6wlucrpg.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Thu, May 11, 2017, Thakur, Abhishek wrote:
> >
> > I have been doing
> >
> > tleap -s -f leaprc.ff14SB.ORIG
> > source leaprc.gaff
> > loadamberparams UNK.frcmod
> > loadoff UNK.lib
> > Na = loadmol2 Na.mol2
> > Cl = loadmol2 Cl.mol2
> > R_config = loadpdb C8_2.pdb
> > solvateBox R_config TIP3PBOX 10
> > charge R_config
> > addIons R_config Cl- 2
> > loadAmberParams frcmod.ionsjc_tip3p
> > saveamberparm R_config C8.prmtop C8.inpcrd
> > savepdb R_config complex.pdb
> > quit
>
> OK: you are rolling your own commands, and are pretty much on your own
> to see what is going wrong.  Consider using standard leaprc files (e.g.
> leaprc.protein.ff14SB, leaprc.water.tip3p).
>
> I note that you called chloride "Cl" in the loadmol2 command, but called
> it "Cl-" in the addIons command.  Look carefully at the leap.log file to
> see exactly what is going on.
>
> Here's my best guess: you get the error for "Na" because the Amber
> libraries
> recognize "NA" and "Na+" (for backward compatibility), but don't have any
> entries for "Na".  There was no error for chloride because of the above
> typo
> in the addIons command.  Easiest fix is probably to edit your pdb file
> and use "NA" and "CL" for sodium and chloride ions.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 11
> Date: Fri, 12 May 2017 22:27:53 +0530
> From: Charles Mariasoosai <charlesmariasoosai51.gmail.com>
> Subject: [AMBER] EEL and VDW Notification on minimization with
>         sander/pmemd
> To: amber.ambermd.org
> Message-ID:
>         <CABu9AX134b3DdUPKPTUCddRYO-AC0YcjJF1Ynv2qed_i7Bo=aw.mail.gm
> ail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Am new to amber.
> i have generated parameters for non standard(modified: covalently attached
> with co-factor ) amino acid and included in my library.
> i have successfully generated prmtop and inpcrd files.
> While running minimisation am getting the folwing notification in out file
> and my minimisation is not proceeding forward?
>
>
>
>
>
>
>
> *| Note: 1-4 EEL scale factors are being read from the topology file.|
> Note: 1-4 VDW scale factors are being read from the topology file. Found a
> non-zero 10-12 coefficient, but source  was not compiled with
> -DHAS_10_12. If you are using a pre-1994 force field, you  will need to
> re-compile with this flag.*
>
>
> how i should solve this ?
> and am getting segmentaion fault in terminal.
>
>
>
> --
>
> *-Regards-*
>
> *?. ???? ?????? ???????(M.Ramya Chandar Charles*)
> Research Scholar
> c/o Dr. S. Mohane Coumar
> Centre for Bioinformatics
> Pondicherry university
> Mob: +91-9283684619
>
>
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> End of AMBER Digest, Vol 1932, Issue 1
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