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-- *Regards* Garima Singh AcSIR-PhD Fellow Biotechnology Division C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division) 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 ! On Tue, May 23, 2017 at 12:47 PM, Garima Singh <garimabioinfo.gmail.com> wrote: > Dear Martis , > As per your previous mail, we have tried that sample script > to run Amber, but this time error message was "command mpirun not found". > The modified script was > > > #! /bin/csh > #PBS -l walltime=10:00:00 > #PBS -N my_job > #PBS -q workq > #PBS -l select=1:ncpus=16:mpiprocs=16 > #PBS -l place=scatter:excl > #PBS -V > > # Go to the directory from which you submitted the job > cd $PBS_O_WORKDIR > > source /home/ashoks/amber14/amber14/amber.csh > > mpirun -np 16 sander.MPI -O -i Prod.in -o Prod.out -p cd_cdat7.prmtop -c > Heat.rst -r prod.rst -x prod.mdcrd -inf prod.info & > > and our working directory was : /home/ashoks/5_garima/at550l/ > > Please do the needful. > > > > > > > > > *Thank You and Best Wishes* > -- > *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_I >> QN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=nKxpXK4_KFVej2ezr8KcHwKSqr >> 8tIcHT_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 Jun 06 2017 - 02:00:03 PDT