[gmx-users] part number in extending simulation
Hi,
Is part number in extending simulation in ver.4.5.4 cancelled?
Below is my shell script,
#!/bin/bash
a=/stathome/jiangsl/simulation/gromacs/d1GUJ_AB/4md
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.5.4/bin/mdrun \
-nt 12 \
-s ${a}/md100ns.tpr \
-o ${a}/md100ns.trr \
-e ${a}/md100ns.edr \
-g ${a}/md100ns.log \
-c ${a}/md100ns.gro \
-cpo ${a}/md100ns.cpt \
-cpi ${a}/md50ns.cpt
#
In GROMACS ver.4.0.5, if I use this script I'll get files such as
md100ns.part002.trr,
md100ns.part002.gro, md100ns.part002.edr, and md100ns.part002.log.
But in ver.4.5.4 I only get md100ns.trr, md100ns.gro, md100ns.edr, and
md100ns.log.
So, is the function of part number in extending simulation in ver.4.5.4
cancelled?
Hsin-Lin
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Re: [gmx-users] Error from residues added to rtp file
On 27/08/2011 2:42 AM, Delmotte, Antoine wrote: Oh, thank you so much! That was indeed the error. It's amazing how these little things can sometimes drive you mad I think the real lesson is to learn to edit documents that will contain nothing but text using an editor that can be relied upon to produce only plain text. Otherwise you spend your valuable time managing things that computer programs should be managing for you. Mark Thanks a lot, Antoine On 08/26/2011 05:27 PM, Thomas Piggot wrote: Hi, I think the problem is that you have a dash rather than a minus symbol for the sign of the charge on the OD atom. Cheers Tom Delmotte, Antoine wrote: Dear Gromacs users, I am currently trying to run an MD simulation with the OPLS-AA force field on a protein having different non standard residues and a ligand. I found the charges for the OPLS force field for these residues in the literature and I am now trying to add them in the OPLS force field parameter files. I have edited the aminoacids.rtp and the aminoacids.hdb files for the OPLS-AA force field, as well as the residuetypes.dat file. Here is an example for one of the amino acids, hydroxyproline: [ HYP ] [ atoms ] N opls_239 -0.140 1 CA opls_246 0.010 1 HA opls_140 0.060 1 CB opls_136 -0.120 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CG opls_137 -0.120 3 HG1 opls_140 0.060 3 OD opls_167 −0.683 3 HD opls_168 0.743 3 CD opls_245 -0.050 4 HD1 opls_140 0.060 4 HD2 opls_140 0.060 4 C opls_235 0.500 5 O opls_236 -0.500 5 [ bonds ] N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG OD OD HD CG CD CD HD1 CD HD2 CD N C O -C N [ impropers ] -C CA N CD improper_Z_N_X_Y CA +N C O improper_O_C_X_Y When I run pdb2gmx, I get the following error, which is not very informative: All occupancies are one Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residue 58 --- Program g_pdb2gmx, VERSION 4.5.3 Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/kernel/resall.c, line: 389 Fatal error: in .rtp file in residue HYP at line: OD opls_167 −0.683 3 I would be grateful if anyone could shed some light on the origin of this error, and on what I can do to correct it. I am using Gromacs 4.5.3. Thanks a lot in advance, Antoine -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Free energy
g_lie calculates the deltaG= alpha(Vl-s LJp - Vl-s LJw) + beta(Vl-s elp - Vl-s elw) equation. But when calculating DGbind from g_lie it will ask for only one term at a time i.e. -Elj for either Vl-s LJp or Vl-s LJw and -Cqq for either Vl-s elp or Vl-s elw. My question is when using only Vl-s LJp for -Elj and Vl-s elp for -Cqq, how the LJ and EL terms calculated for ligand-water interaction or in vice-versa condition for ligand-protein interactions to complete the deltaG equation? -- Pawan -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] part number in extending simulation
On Sun, 2011-08-28 at 14:21 +0800, Hsin-Lin Chiang wrote:
Hi,
Is part number in extending simulation in ver.4.5.4 cancelled?
Below is my shell script,
#!/bin/bash
a=/stathome/jiangsl/simulation/gromacs/d1GUJ_AB/4md
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.5.4/bin/mdrun \
-nt 12 \
-s ${a}/md100ns.tpr \
-o ${a}/md100ns.trr \
-e ${a}/md100ns.edr \
-g ${a}/md100ns.log \
-c ${a}/md100ns.gro \
-cpo ${a}/md100ns.cpt \
-cpi ${a}/md50ns.cpt
#
In GROMACS ver.4.0.5, if I use this script I'll get files such as
md100ns.part002.trr,
md100ns.part002.gro, md100ns.part002.edr, and md100ns.part002.log.
But in ver.4.5.4 I only get md100ns.trr, md100ns.gro, md100ns.edr, and
md100ns.log.
So, is the function of part number in extending simulation in ver.4.5.4
cancelled?
Hi,
check the standard options of mdrun with the help flag -h of version
4.5.4 and below. You will realize, that the standard append behaviour
changed from no to yes. Hence if you start from a checkpoint and
files are already present in the working directory the integration
results will be appended.
/Flo
Hsin-Lin
--
Florian Dommert
Dipl. - Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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[gmx-users] part number in extending simulation
Hi Flo, Thank you for reply. I got it. But as you see I also indicate the new names for output files. Do I get correct result in this kind of situation? Or I need to rerun it with -noappend Sincerely yours, Hsin-Lin Hi, check the standard options of mdrun with the help flag -h of version 4.5.4 and below. You will realize, that the standard append behaviour changed from no to yes. Hence if you start from a checkpoint and files are already present in the working directory the integration results will be appended. Flo -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] part number in extending simulation
On Sun, 2011-08-28 at 17:55 +0800, Hsin-Lin Chiang wrote: Hi Flo, Thank you for reply. I got it. But as you see I also indicate the new names for output files. Do I get correct result in this kind of situation? Or I need to rerun it with -noappend I am not sure, but I assume if you set new names, new files will be created. The checkpoint input files contains important information about your coordinates, velocities, states of random number generators for the NH coupling That is the reason, why it is necessary for a continuous extension of your run. The results should not depend on the append option, only the number of resulting trajectories is affected. The suffix part??? will just arise if the files are already present and you use -noappend. Now you will end up with two trajectories I assume: * md50ns, * md100ns, which are indistinguishable from a single continuous 100ns run and I think that is what you want, isn't it ? /Flo Sincerely yours, Hsin-Lin Hi, check the standard options of mdrun with the help flag -h of version 4.5.4 and below. You will realize, that the standard append behaviour changed from no to yes. Hence if you start from a checkpoint and files are already present in the working directory the integration results will be appended. Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] part number in extending simulation
I am not sure, but I assume if you set new names, new files will be created. The checkpoint input files contains important information about your coordinates, velocities, states of random number generators for the NH coupling That is the reason, why it is necessary for a continuous extension of your run. The results should not depend on the append option, only the number of resulting trajectories is affected. The suffix part??? will just arise if the files are already present and you use -noappend. Now you will end up with two trajectories I assume: * md50ns, * md100ns, which are indistinguishable from a single continuous 100ns run and I think that is what you want, isn't it ? /Flo Thank you. I'm not sure,too. Exactly mdrun create md100ns.trr for me, but I'm not sure if any thing is right in the file. So I added -noappend to rerun it again and this result will be correct without doubt. By the way, md100ns.trr here mean from 50ns to 100ns. I just don't want the new run append to md50ns.trr to make me confused. Hsin-Lin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] distance between mass center of two groups
Dear users, is there any command in Gromacs to show fluctuations of distance, between mass center for two groups of amino-acids in a protein, over time? thanks, sajad-- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] distance between mass center of two groups
Use g_dist tool. On Sun, Aug 28, 2011 at 8:38 AM, Sajad Ahrari sajadahr...@yahoo.com wrote: Dear users, is there any command in Gromacs to show fluctuations of distance, between mass center for two groups of amino-acids in a protein, over time? thanks, sajad -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] distance between mass center of two groups
On 29/08/2011 1:38 AM, Sajad Ahrari wrote: Dear users, is there any command in Gromacs to show fluctuations of distance, between mass center for two groups of amino-acids in a protein, over time? Check out manual section 7.4 for clues about which tools do what, and chapter 8 for more detail. Mark -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] amber DNA non-integer charge
Hil, I am trying to simulate a protein-DNA structure using amber03 and end up having a non-integer charge in topology generation . From the webpage of ffamber on NA-simulations, I could see this below instruction However, for nucleic acids this also often causes pdb2gmx to replace an H atom in the first residue of all nucleic acid chains with an incorrect H atom, resulting in non-neutral charge. The correct atom is generally replaced with an atom of type amberXX_25 (hydroxyl H), as pdb2gmx treats it as a terminal hydrogen. I replaced the aminoacids.dat contents with aminoacids-NA.dat contents and therefore not sure how the non-integer originates. In my top file I can see this residue of the type amber99_25 . How do I correct for the atom-type and charge in this case ? amber99_25 1DG5H5T 2 0.4422 1.008 ; qtot -0.1896 My top file section: nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 amber99_43 1DG5O5' 1-0.6318 16 ; qtot -0.6318 2 amber99_25 1DG5H5T 2 0.4422 1.008 ; qtot -0.1896 3 amber99_11 1DG5C5' 3-0.0069 12.01 ; qtot -0.1965 4 amber99_19 1DG5 H5'1 4 0.0754 1.008 ; qtot -0.1211 5 amber99_19 1DG5 H5'2 5 0.0754 1.008 ; qtot -0.0457 6 amber99_11 1DG5C4' 6 0.1629 12.01 ; qtot 0.1172 7 amber99_19 1DG5H4' 7 0.1176 1.008 ; qtot 0.2348 8 amber99_44 1DG5O4' 8-0.3691 16 ; qtot -0.1343 9 amber99_11 1DG5C1' 9 0.0358 12.01 ; qtot -0.0985 10 amber99_20 1DG5H1' 10 0.1746 1.008 ; qtot 0.0761 11 amber99_40 1DG5 N9 11 0.0577 14.01 ; qtot 0.1338 12 amber99_6 1DG5 C8 12 0.0736 12.01 ; qtot 0.2074 13 amber99_24 1DG5 H8 13 0.1997 1.008 ; qtot 0.4071 14 amber99_36 1DG5 N7 14-0.5725 14.01 ; qtot -0.1654 15 amber99_4 1DG5 C5 15 0.1991 12.01 ; qtot 0.0337 16 amber99_2 1DG5 C6 16 0.4918 12.01 ; qtot 0.5255 17 amber99_41 1DG5 O6 17-0.5699 16 ; qtot -0.0444 18 amber99_35 1DG5 N1 18-0.5053 14.01 ; qtot -0.5497 19 amber99_25 1DG5 H1 19 0.4422 1.008 ; qtot -0.1075 20 amber99_3 1DG5 C2 20 0.7432 12.01 ; qtot 0.6357 21 amber99_38 1DG5 N2 21 -0.923 14.01 ; qtot -0.2873 22 amber99_17 1DG5H21 22 0.4235 1.008 ; qtot 0.1362 23 amber99_17 1DG5H22 23 0.4235 1.008 ; qtot 0.5597 24 amber99_37 1DG5 N3 24-0.6636 14.01 ; qtot -0.1039 25 amber99_4 1DG5 C4 25 0.1814 12.01 ; qtot 0.0775 26 amber99_11 1DG5C3' 26 0.0713 12.01 ; qtot 0.1488 27 amber99_19 1DG5H3' 27 0.0985 1.008 ; qtot 0.2473 28 amber99_11 1DG5C2' 28-0.0854 12.01 ; qtot 0.1619 29 amber99_18 1DG5 H2'1 29 0.0718 1.008 ; qtot 0.2337 30 amber99_18 1DG5 H2'2 30 0.0718 1.008 ; qtot 0.3055 31 amber99_44 1DG5O3' 31-0.5232 16 ; qtot -0.2177 . My pdb file section: ATOM 1 C5' DG5 A 1 28.937 -10.596 -28.986 1.00 95.46 C ATOM 2 O5' DG5 A 1 30.060 -10.216 -29.774 1.00 95.82 O ATOM 3 C4' DG5 A 1 29.239 -11.863 -28.212 1.00101.28 C ATOM 4 O4' DG5 A 1 30.545 -11.736 -27.597 1.00102.88 O ATOM 5 C3' DG5 A 1 28.300 -12.150 -27.052 1.00100.37 C ATOM 6 O3' DG5 A 1 28.363 -13.527 -26.704 1.00104.13 O ATOM 7 C2' DG5 A 1 28.913 -11.282 -25.960 1.00 95.28 C ATOM 8 C1' DG5 A 1 30.395 -11.553 -26.200 1.00100.67 C ATOM 9 N1 DG5 A 1 34.400 -10.292 -23.339 1.00 88.74 N ATOM 10 C2 DG5 A 1 33.795 -11.515 -23.502 1.00 92.09 C ATOM 11 N2 DG5 A 1 34.320 -12.542 -22.818 1.00 92.20 N ATOM 12 N3 DG5 A 1 32.745 -11.722 -24.284 1.00100.66 N ATOM 13 C4 DG5 A 1 32.342 -10.585 -24.901 1.00101.19 C ATOM 14 C5 DG5 A 1 32.877 -9.321 -24.804 1.00 97.04 C ATOM 15 C6 DG5 A 1 33.999 -9.114 -23.965 1.00 93.19 C ATOM 16 O6 DG5 A 1 34.613 -8.059 -23.751 1.00 94.32 O ATOM 17 N7 DG5 A 1 32.171 -8.426
Re: [gmx-users] amber DNA non-integer charge
Kamesh Narasimhan wrote: Hil, I am trying to simulate a protein-DNA structure using amber03 and end up having a non-integer charge in topology generation . From the webpage of ffamber on NA-simulations, I could see this below instruction However, for nucleic acids this also often causes pdb2gmx to replace an H atom in the first residue of all nucleic acid chains with an incorrect H atom, resulting in non-neutral charge. The correct atom is generally replaced with an atom of type amberXX_25 (hydroxyl H), as pdb2gmx treats it as a terminal hydrogen. I replaced the aminoacids.dat contents with aminoacids-NA.dat contents and therefore not sure how the non-integer originates. In my top file I can see this residue of the type amber99_25 . How do I correct for the atom-type and charge in this case ? amber99_25 1DG5H5T 2 0.4422 1.008 ; qtot -0.1896 My top file section: nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 amber99_43 1DG5O5' 1-0.6318 16 ; qtot -0.6318 2 amber99_25 1DG5H5T 2 0.4422 1.008 ; qtot -0.1896 3 amber99_11 1DG5C5' 3-0.0069 12.01 ; qtot -0.1965 4 amber99_19 1DG5 H5'1 4 0.0754 1.008 ; qtot -0.1211 5 amber99_19 1DG5 H5'2 5 0.0754 1.008 ; qtot -0.0457 6 amber99_11 1DG5C4' 6 0.1629 12.01 ; qtot 0.1172 7 amber99_19 1DG5H4' 7 0.1176 1.008 ; qtot 0.2348 8 amber99_44 1DG5O4' 8-0.3691 16 ; qtot -0.1343 9 amber99_11 1DG5C1' 9 0.0358 12.01 ; qtot -0.0985 10 amber99_20 1DG5H1' 10 0.1746 1.008 ; qtot 0.0761 11 amber99_40 1DG5 N9 11 0.0577 14.01 ; qtot 0.1338 12 amber99_6 1DG5 C8 12 0.0736 12.01 ; qtot 0.2074 13 amber99_24 1DG5 H8 13 0.1997 1.008 ; qtot 0.4071 14 amber99_36 1DG5 N7 14-0.5725 14.01 ; qtot -0.1654 15 amber99_4 1DG5 C5 15 0.1991 12.01 ; qtot 0.0337 16 amber99_2 1DG5 C6 16 0.4918 12.01 ; qtot 0.5255 17 amber99_41 1DG5 O6 17-0.5699 16 ; qtot -0.0444 18 amber99_35 1DG5 N1 18-0.5053 14.01 ; qtot -0.5497 19 amber99_25 1DG5 H1 19 0.4422 1.008 ; qtot -0.1075 The charge on H1 is wrong. According to the DG5 .rtp entry (in the version 4.5.x series), the charge should be 0.352. -Justin 20 amber99_3 1DG5 C2 20 0.7432 12.01 ; qtot 0.6357 21 amber99_38 1DG5 N2 21 -0.923 14.01 ; qtot -0.2873 22 amber99_17 1DG5H21 22 0.4235 1.008 ; qtot 0.1362 23 amber99_17 1DG5H22 23 0.4235 1.008 ; qtot 0.5597 24 amber99_37 1DG5 N3 24-0.6636 14.01 ; qtot -0.1039 25 amber99_4 1DG5 C4 25 0.1814 12.01 ; qtot 0.0775 26 amber99_11 1DG5C3' 26 0.0713 12.01 ; qtot 0.1488 27 amber99_19 1DG5H3' 27 0.0985 1.008 ; qtot 0.2473 28 amber99_11 1DG5C2' 28-0.0854 12.01 ; qtot 0.1619 29 amber99_18 1DG5 H2'1 29 0.0718 1.008 ; qtot 0.2337 30 amber99_18 1DG5 H2'2 30 0.0718 1.008 ; qtot 0.3055 31 amber99_44 1DG5O3' 31-0.5232 16 ; qtot -0.2177 . My pdb file section: ATOM 1 C5' DG5 A 1 28.937 -10.596 -28.986 1.00 95.46 C ATOM 2 O5' DG5 A 1 30.060 -10.216 -29.774 1.00 95.82 O ATOM 3 C4' DG5 A 1 29.239 -11.863 -28.212 1.00101.28 C ATOM 4 O4' DG5 A 1 30.545 -11.736 -27.597 1.00102.88 O ATOM 5 C3' DG5 A 1 28.300 -12.150 -27.052 1.00100.37 C ATOM 6 O3' DG5 A 1 28.363 -13.527 -26.704 1.00104.13 O ATOM 7 C2' DG5 A 1 28.913 -11.282 -25.960 1.00 95.28 C ATOM 8 C1' DG5 A 1 30.395 -11.553 -26.200 1.00100.67 C ATOM 9 N1 DG5 A 1 34.400 -10.292 -23.339 1.00 88.74 N ATOM 10 C2 DG5 A 1 33.795 -11.515 -23.502 1.00 92.09 C ATOM 11 N2 DG5 A 1 34.320 -12.542 -22.818 1.00 92.20 N ATOM 12 N3 DG5 A 1 32.745 -11.722 -24.284 1.00100.66 N ATOM 13 C4 DG5 A 1 32.342 -10.585 -24.901 1.00101.19 C ATOM 14 C5 DG5 A 1 32.877 -9.321 -24.804 1.00 97.04 C ATOM 15 C6 DG5 A 1 33.999 -9.114
RE: [gmx-users] amber DNA non-integer charge
I am using Gromacs 4.0.5 and in my ffamber03.rtp I can see that the charges are as you mentioned. H1amber99_170.3520019 But in my top file the H1 atom of the type amber99_17 gets replaced by the amber99_25 type so what should have been amber99_17 1DG5 H1 19 0.352001.008 ; is written by pdb2gmx as amber99_25 1DG5 H1 19 0.4422 1.008 ; How can I make amber generate the topology with the right atomtype and charge in this case?. Thanks in advance. my top file: 1 amber99_43 1DG5O5' 1-0.6318 16 ; qtot -0.6318 2 amber99_25 1DG5H5T 2 0.4422 1.008 ; qtot -0.1896 3 amber99_11 1DG5C5' 3-0.0069 12.01 ; qtot -0.1965 4 amber99_19 1DG5 H5'1 4 0.0754 1.008 ; qtot -0.1211 5 amber99_19 1DG5 H5'2 5 0.0754 1.008 ; qtot -0.0457 6 amber99_11 1DG5C4' 6 0.1629 12.01 ; qtot 0.1172 7 amber99_19 1DG5H4' 7 0.1176 1.008 ; qtot 0.2348 8 amber99_44 1DG5O4' 8-0.3691 16 ; qtot -0.1343 9 amber99_11 1DG5C1' 9 0.0358 12.01 ; qtot -0.0985 10 amber99_20 1DG5H1' 10 0.1746 1.008 ; qtot 0.0761 11 amber99_40 1DG5 N9 11 0.0577 14.01 ; qtot 0.1338 12 amber99_6 1DG5 C8 12 0.0736 12.01 ; qtot 0.2074 13 amber99_24 1DG5 H8 13 0.1997 1.008 ; qtot 0.4071 14 amber99_36 1DG5 N7 14-0.5725 14.01 ; qtot -0.1654 15 amber99_4 1DG5 C5 15 0.1991 12.01 ; qtot 0.0337 16 amber99_2 1DG5 C6 16 0.4918 12.01 ; qtot 0.5255 17 amber99_41 1DG5 O6 17-0.5699 16 ; qtot -0.0444 18 amber99_35 1DG5 N1 18-0.5053 14.01 ; qtot -0.5497 19 amber99_25 1DG5 H1 19 0.4422 1.008 ; qtot -0.1075 20 amber99_3 1DG5 C2 20 0.7432 12.01 ; qtot 0.6357 21 amber99_38 1DG5 N2 21 -0.923 14.01 ; qtot -0.2873 22 amber99_17 1DG5H21 22 0.4235 1.008 ; qtot 0.1362 23 amber99_17 1DG5H22 23 0.4235 1.008 ; qtot 0.5597 24 amber99_37 1DG5 N3 24-0.6636 14.01 ; qtot -0.1039 25 amber99_4 1DG5 C4 25 0.1814 12.01 ; qtot 0.0775 26 amber99_11 1DG5C3' 26 0.0713 12.01 ; qtot 0.1488 27 amber99_19 1DG5H3' 27 0.0985 1.008 ; qtot 0.2473 28 amber99_11 1DG5C2' 28-0.0854 12.01 ; qtot 0.1619 29 amber99_18 1DG5 H2'1 29 0.0718 1.008 ; qtot 0.2337 30 amber99_18 1DG5 H2'2 30 0.0718 1.008 ; qtot 0.3055 31 amber99_44 1DG5O3' 31-0.5232 16 ; qtot -0.2177 . ... . From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, August 29, 2011 2:41 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] amber DNA non-integer charge Kamesh Narasimhan wrote: Hil, I am trying to simulate a protein-DNA structure using amber03 and end up having a non-integer charge in topology generation . From the webpage of ffamber on NA-simulations, I could see this below instruction However, for nucleic acids this also often causes pdb2gmx to replace an H atom in the first residue of all nucleic acid chains with an incorrect H atom, resulting in non-neutral charge. The correct atom is generally replaced with an atom of type amberXX_25 (hydroxyl H), as pdb2gmx treats it as a terminal hydrogen. I replaced the aminoacids.dat contents with aminoacids-NA.dat contents and therefore not sure how the non-integer originates. In my top file I can see this residue of the type amber99_25 . How do I correct for the atom-type and charge in this case ? amber99_25 1DG5H5T 2 0.4422 1.008 ; qtot -0.1896 My top file section: nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 amber99_43 1DG5O5' 1-0.6318 16 ; qtot -0.6318 2 amber99_25 1DG5H5T 2 0.4422 1.008 ; qtot -0.1896 3 amber99_11 1DG5C5' 3-0.0069 12.01 ; qtot -0.1965 4 amber99_19 1DG5 H5'1 4 0.0754 1.008 ; qtot -0.1211 5 amber99_19 1DG5 H5'2 5 0.0754 1.008 ; qtot -0.0457 6 amber99_11 1
Re: [gmx-users] amber DNA non-integer charge
Kamesh Narasimhan wrote: I am using Gromacs 4.0.5 and in my ffamber03.rtp I can see that the charges are as you mentioned. H1amber99_170.3520019 But in my top file the H1 atom of the type amber99_17 gets replaced by the amber99_25 type so what should have been amber99_17 1DG5 H1 19 0.352001.008 ; is written by pdb2gmx as amber99_25 1DG5 H1 19 0.4422 1.008 ; How can I make amber generate the topology with the right atomtype and charge in this case?. Thanks in advance. I don't know, but it's not productive to troubleshoot buggy behavior in a Gromacs version that is over two years old. I'd suggest upgrading to the newest version (4.5.4, with the appropriate version of the Amber ports) and seeing if the behavior persists. Otherwise, edit the topology manually to correct the error. -Justin my top file: 1 amber99_43 1DG5O5' 1-0.6318 16 ; qtot -0.6318 2 amber99_25 1DG5H5T 2 0.4422 1.008 ; qtot -0.1896 3 amber99_11 1DG5C5' 3-0.0069 12.01 ; qtot -0.1965 4 amber99_19 1DG5 H5'1 4 0.0754 1.008 ; qtot -0.1211 5 amber99_19 1DG5 H5'2 5 0.0754 1.008 ; qtot -0.0457 6 amber99_11 1DG5C4' 6 0.1629 12.01 ; qtot 0.1172 7 amber99_19 1DG5H4' 7 0.1176 1.008 ; qtot 0.2348 8 amber99_44 1DG5O4' 8-0.3691 16 ; qtot -0.1343 9 amber99_11 1DG5C1' 9 0.0358 12.01 ; qtot -0.0985 10 amber99_20 1DG5H1' 10 0.1746 1.008 ; qtot 0.0761 11 amber99_40 1DG5 N9 11 0.0577 14.01 ; qtot 0.1338 12 amber99_6 1DG5 C8 12 0.0736 12.01 ; qtot 0.2074 13 amber99_24 1DG5 H8 13 0.1997 1.008 ; qtot 0.4071 14 amber99_36 1DG5 N7 14-0.5725 14.01 ; qtot -0.1654 15 amber99_4 1DG5 C5 15 0.1991 12.01 ; qtot 0.0337 16 amber99_2 1DG5 C6 16 0.4918 12.01 ; qtot 0.5255 17 amber99_41 1DG5 O6 17-0.5699 16 ; qtot -0.0444 18 amber99_35 1DG5 N1 18-0.5053 14.01 ; qtot -0.5497 19 amber99_25 1DG5 H1 19 0.4422 1.008 ; qtot -0.1075 20 amber99_3 1DG5 C2 20 0.7432 12.01 ; qtot 0.6357 21 amber99_38 1DG5 N2 21 -0.923 14.01 ; qtot -0.2873 22 amber99_17 1DG5H21 22 0.4235 1.008 ; qtot 0.1362 23 amber99_17 1DG5H22 23 0.4235 1.008 ; qtot 0.5597 24 amber99_37 1DG5 N3 24-0.6636 14.01 ; qtot -0.1039 25 amber99_4 1DG5 C4 25 0.1814 12.01 ; qtot 0.0775 26 amber99_11 1DG5C3' 26 0.0713 12.01 ; qtot 0.1488 27 amber99_19 1DG5H3' 27 0.0985 1.008 ; qtot 0.2473 28 amber99_11 1DG5C2' 28-0.0854 12.01 ; qtot 0.1619 29 amber99_18 1DG5 H2'1 29 0.0718 1.008 ; qtot 0.2337 30 amber99_18 1DG5 H2'2 30 0.0718 1.008 ; qtot 0.3055 31 amber99_44 1DG5O3' 31-0.5232 16 ; qtot -0.2177 . ... . From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, August 29, 2011 2:41 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] amber DNA non-integer charge Kamesh Narasimhan wrote: Hil, I am trying to simulate a protein-DNA structure using amber03 and end up having a non-integer charge in topology generation . From the webpage of ffamber on NA-simulations, I could see this below instruction However, for nucleic acids this also often causes pdb2gmx to replace an H atom in the first residue of all nucleic acid chains with an incorrect H atom, resulting in non-neutral charge. The correct atom is generally replaced with an atom of type amberXX_25 (hydroxyl H), as pdb2gmx treats it as a terminal hydrogen. I replaced the aminoacids.dat contents with aminoacids-NA.dat contents and therefore not sure how the non-integer originates. In my top file I can see this residue of the type amber99_25 . How do I correct for the atom-type and charge in this case ? amber99_25 1DG5H5T 2 0.4422 1.008 ; qtot -0.1896 My top file section: nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 amber99_43 1DG5O5' 1-0.6318 16 ; qtot -0.6318 2 amber99_25 1DG5H5T
