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-- *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 > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.ambermd.org/mailman/listinfo/amber > or, via email, send a message with subject or body 'help' to > amber-request.ambermd.org > > You can reach the person managing the list at > amber-owner.ambermd.org > > 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 > > > > > *INDIA* Please don't print this e-mail unless you really need to. Be Green > ! > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > ------------------------------ > > 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 > > > ------------------------------ > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > > End of AMBER Digest, Vol 1932, Issue 1 > ************************************** > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue May 23 2017 - 00:30:02 PDT