Re: [gmx-users] Residue not found in topology
On 8/23/18 8:12 AM, Amir Zeb wrote: Thanks Justin, I have followed what did you suggest for .rtp entry in merged.rtp file of charmm36 ff. But i could not make .hdb file for ALY. Where can i find the H-information for ALY to insert them in merged.hdb file of charmm36 ff? Look at existing residues and consult the relevant portion of the GROMACS manual. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Residue not found in topology
Thanks Justin, I have followed what did you suggest for .rtp entry in merged.rtp file of charmm36 ff. But i could not make .hdb file for ALY. Where can i find the H-information for ALY to insert them in merged.hdb file of charmm36 ff? Amir On Thu, Aug 23, 2018, 9:02 PM Justin Lemkul wrote: > > > On 8/23/18 7:52 AM, Bratin Kumar Das wrote: > > Hi > > You can see that only the problem is coming from hydrogen. So in > pdb2gmx > > command use -ignh so that it ignores the hydrogen. If you use this this > > WARNING will not come. > > That's not true. The -ignh option ignores H atoms in the input > coordinate file and is useful when there are H atoms with names that do > not agree with what is specified in the .rtp entry for the given > residue. The OP's problem is the opposite: the H are not there but need > to be built. > > -Justin > > > On Fri, Aug 24, 2018 at 4:00 AM, Amir Zeb wrote: > > > >> Thanks Justin, > >> > >> Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/ > and > >> generated the parameters for KAC. > >> The merged.rtp file was modified by adding the KAC parameters > >> That issue fixed, but now I'm getting the following warning which > >> ultimately results in fatal error. > >> > >> WARNING: atom HA is missing in residue KAC 33 in the pdb file > >> You might need to add atom HA to the hydrogen database of > building > >> block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HB1 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HB1 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HB2 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HB2 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HG1 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HG1 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HG2 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HG2 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HD1 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HD1 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HD2 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HD2 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HE1 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HE1 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HE2 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HE2 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HZ1 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HZ1 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HI11 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HI11 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HI12 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HI12 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HI13 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HI13 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HZ2 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HZ2 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> > >> WARNING: atom HT2 is missing in residue KAC 33 in the pdb file > >> You might need to add atom HT2 to the hydrogen database of > >> building block KAC > >> in the file merged.hdb (see the manual) > >> > >> How may I fix this issue? > >> > >> Thanks in advance! > >> > >> > >> On Wed, Aug 22, 2018 at 4:31 AM Justin Lemkul wrote: > >> > >>> > >>> On 8/22/18 5:26 AM, Bratin Kumar Das wrote: > Hi > In your tool.top file the particular lys molecule residue name > you > >>> have >
Re: [gmx-users] Residue not found in topology
On 8/23/18 7:52 AM, Bratin Kumar Das wrote: Hi You can see that only the problem is coming from hydrogen. So in pdb2gmx command use -ignh so that it ignores the hydrogen. If you use this this WARNING will not come. That's not true. The -ignh option ignores H atoms in the input coordinate file and is useful when there are H atoms with names that do not agree with what is specified in the .rtp entry for the given residue. The OP's problem is the opposite: the H are not there but need to be built. -Justin On Fri, Aug 24, 2018 at 4:00 AM, Amir Zeb wrote: Thanks Justin, Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/ and generated the parameters for KAC. The merged.rtp file was modified by adding the KAC parameters That issue fixed, but now I'm getting the following warning which ultimately results in fatal error. WARNING: atom HA is missing in residue KAC 33 in the pdb file You might need to add atom HA to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HB1 is missing in residue KAC 33 in the pdb file You might need to add atom HB1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HB2 is missing in residue KAC 33 in the pdb file You might need to add atom HB2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HG1 is missing in residue KAC 33 in the pdb file You might need to add atom HG1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HG2 is missing in residue KAC 33 in the pdb file You might need to add atom HG2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HD1 is missing in residue KAC 33 in the pdb file You might need to add atom HD1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HD2 is missing in residue KAC 33 in the pdb file You might need to add atom HD2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HE1 is missing in residue KAC 33 in the pdb file You might need to add atom HE1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HE2 is missing in residue KAC 33 in the pdb file You might need to add atom HE2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HZ1 is missing in residue KAC 33 in the pdb file You might need to add atom HZ1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HI11 is missing in residue KAC 33 in the pdb file You might need to add atom HI11 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HI12 is missing in residue KAC 33 in the pdb file You might need to add atom HI12 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HI13 is missing in residue KAC 33 in the pdb file You might need to add atom HI13 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HZ2 is missing in residue KAC 33 in the pdb file You might need to add atom HZ2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HT2 is missing in residue KAC 33 in the pdb file You might need to add atom HT2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) How may I fix this issue? Thanks in advance! On Wed, Aug 22, 2018 at 4:31 AM Justin Lemkul wrote: On 8/22/18 5:26 AM, Bratin Kumar Das wrote: Hi In your tool.top file the particular lys molecule residue name you have to modify. Then it will work..Actually grompp can't find the molecule in the topology. The error has nothing to do with grompp. The topology was never created because pdb2gmx could not write a topology for KAC. CHARMM36 does support KAC, but not as a standalone residue. In CHARMM, one would generate a normal lysine then patch it with the KAC patch. To make this work in GROMACS, one would have to create a KAC .rtp entry by applying the same logic - modify LYS according to the KAC patch (found in the stream/prot/toppar_all36_prot_modify_res.str file from the tarball distributed by Alex MacKerell: http://mackerell.umaryland.edu/charmm_ff.shtml#charmm). -Justin On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, < 177cy500.bra...@nitk.edu.in> wrote: Hi In your tool.top file the particular lys molecule residue name you have to
Re: [gmx-users] Residue not found in topology
On 8/23/18 6:30 PM, Amir Zeb wrote: Thanks Justin, Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/ and generated the parameters for KAC. Do not generate parameters in this way. You will have a mixture of highly optimized protein parameters for all other residues, then the CGenFF version of KAC. CGenFF parameters are inherently a trade-off between optimization and transferability. You'll also end up with a hodge-podge of bonded parameters that will need to be added and/or reoptimized to link this residue to its neighbors. Please follow what I said before and create a proper .rtp entry. It is quite simple. The merged.rtp file was modified by adding the KAC parameters That issue fixed, but now I'm getting the following warning which ultimately results in fatal error. WARNING: atom HA is missing in residue KAC 33 in the pdb file You might need to add atom HA to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HB1 is missing in residue KAC 33 in the pdb file You might need to add atom HB1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HB2 is missing in residue KAC 33 in the pdb file You might need to add atom HB2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HG1 is missing in residue KAC 33 in the pdb file You might need to add atom HG1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HG2 is missing in residue KAC 33 in the pdb file You might need to add atom HG2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HD1 is missing in residue KAC 33 in the pdb file You might need to add atom HD1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HD2 is missing in residue KAC 33 in the pdb file You might need to add atom HD2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HE1 is missing in residue KAC 33 in the pdb file You might need to add atom HE1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HE2 is missing in residue KAC 33 in the pdb file You might need to add atom HE2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HZ1 is missing in residue KAC 33 in the pdb file You might need to add atom HZ1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HI11 is missing in residue KAC 33 in the pdb file You might need to add atom HI11 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HI12 is missing in residue KAC 33 in the pdb file You might need to add atom HI12 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HI13 is missing in residue KAC 33 in the pdb file You might need to add atom HI13 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HZ2 is missing in residue KAC 33 in the pdb file You might need to add atom HZ2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HT2 is missing in residue KAC 33 in the pdb file You might need to add atom HT2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) How may I fix this issue? You need to create an .hdb entry for the new residue. -Justin Thanks in advance! On Wed, Aug 22, 2018 at 4:31 AM Justin Lemkul wrote: On 8/22/18 5:26 AM, Bratin Kumar Das wrote: Hi In your tool.top file the particular lys molecule residue name you have to modify. Then it will work..Actually grompp can't find the molecule in the topology. The error has nothing to do with grompp. The topology was never created because pdb2gmx could not write a topology for KAC. CHARMM36 does support KAC, but not as a standalone residue. In CHARMM, one would generate a normal lysine then patch it with the KAC patch. To make this work in GROMACS, one would have to create a KAC .rtp entry by applying the same logic - modify LYS according to the KAC patch (found in the stream/prot/toppar_all36_prot_modify_res.str file from the tarball distributed by Alex MacKerell: http://mackerell.umaryland.edu/charmm_ff.shtml#charmm). -Justin On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, < 177cy500.bra...@nitk.edu.in> wrote: Hi In your tool.top file the particular lys molecule residue name
Re: [gmx-users] Residue not found in topology
Hi You can see that only the problem is coming from hydrogen. So in pdb2gmx command use -ignh so that it ignores the hydrogen. If you use this this WARNING will not come. On Fri, Aug 24, 2018 at 4:00 AM, Amir Zeb wrote: > Thanks Justin, > > Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/ and > generated the parameters for KAC. > The merged.rtp file was modified by adding the KAC parameters > That issue fixed, but now I'm getting the following warning which > ultimately results in fatal error. > > WARNING: atom HA is missing in residue KAC 33 in the pdb file > You might need to add atom HA to the hydrogen database of building > block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HB1 is missing in residue KAC 33 in the pdb file > You might need to add atom HB1 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HB2 is missing in residue KAC 33 in the pdb file > You might need to add atom HB2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HG1 is missing in residue KAC 33 in the pdb file > You might need to add atom HG1 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HG2 is missing in residue KAC 33 in the pdb file > You might need to add atom HG2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HD1 is missing in residue KAC 33 in the pdb file > You might need to add atom HD1 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HD2 is missing in residue KAC 33 in the pdb file > You might need to add atom HD2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HE1 is missing in residue KAC 33 in the pdb file > You might need to add atom HE1 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HE2 is missing in residue KAC 33 in the pdb file > You might need to add atom HE2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HZ1 is missing in residue KAC 33 in the pdb file > You might need to add atom HZ1 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HI11 is missing in residue KAC 33 in the pdb file > You might need to add atom HI11 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HI12 is missing in residue KAC 33 in the pdb file > You might need to add atom HI12 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HI13 is missing in residue KAC 33 in the pdb file > You might need to add atom HI13 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HZ2 is missing in residue KAC 33 in the pdb file > You might need to add atom HZ2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HT2 is missing in residue KAC 33 in the pdb file > You might need to add atom HT2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > How may I fix this issue? > > Thanks in advance! > > > On Wed, Aug 22, 2018 at 4:31 AM Justin Lemkul wrote: > > > > > > > On 8/22/18 5:26 AM, Bratin Kumar Das wrote: > > > Hi > > > In your tool.top file the particular lys molecule residue name you > > have > > > to modify. Then it will work..Actually grompp can't find the molecule > in > > > the topology. > > > > The error has nothing to do with grompp. The topology was never created > > because pdb2gmx could not write a topology for KAC. > > > > CHARMM36 does support KAC, but not as a standalone residue. In CHARMM, > > one would generate a normal lysine then patch it with the KAC patch. To > > make this work in GROMACS, one would have to create a KAC .rtp entry by > > applying the same logic - modify LYS according to the KAC patch (found > > in the stream/prot/toppar_all36_prot_modify_res.str file from the > > tarball distributed by Alex MacKerell: > > http://mackerell.umaryland.edu/charmm_ff.shtml#charmm). > > > > -Justin > > > > > On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, < > > 177cy500.bra...@nitk.edu.in> > > > wrote: > > > > > >> Hi > > >> In your tool.top file the particular lys molecule residue name > you > > >> have to modify. Then it will work..Actually grompp can't find the > > molecule > > >> in the
Re: [gmx-users] Residue not found in topology
Thanks Justin, Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/ and generated the parameters for KAC. The merged.rtp file was modified by adding the KAC parameters That issue fixed, but now I'm getting the following warning which ultimately results in fatal error. WARNING: atom HA is missing in residue KAC 33 in the pdb file You might need to add atom HA to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HB1 is missing in residue KAC 33 in the pdb file You might need to add atom HB1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HB2 is missing in residue KAC 33 in the pdb file You might need to add atom HB2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HG1 is missing in residue KAC 33 in the pdb file You might need to add atom HG1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HG2 is missing in residue KAC 33 in the pdb file You might need to add atom HG2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HD1 is missing in residue KAC 33 in the pdb file You might need to add atom HD1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HD2 is missing in residue KAC 33 in the pdb file You might need to add atom HD2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HE1 is missing in residue KAC 33 in the pdb file You might need to add atom HE1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HE2 is missing in residue KAC 33 in the pdb file You might need to add atom HE2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HZ1 is missing in residue KAC 33 in the pdb file You might need to add atom HZ1 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HI11 is missing in residue KAC 33 in the pdb file You might need to add atom HI11 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HI12 is missing in residue KAC 33 in the pdb file You might need to add atom HI12 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HI13 is missing in residue KAC 33 in the pdb file You might need to add atom HI13 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HZ2 is missing in residue KAC 33 in the pdb file You might need to add atom HZ2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) WARNING: atom HT2 is missing in residue KAC 33 in the pdb file You might need to add atom HT2 to the hydrogen database of building block KAC in the file merged.hdb (see the manual) How may I fix this issue? Thanks in advance! On Wed, Aug 22, 2018 at 4:31 AM Justin Lemkul wrote: > > > On 8/22/18 5:26 AM, Bratin Kumar Das wrote: > > Hi > > In your tool.top file the particular lys molecule residue name you > have > > to modify. Then it will work..Actually grompp can't find the molecule in > > the topology. > > The error has nothing to do with grompp. The topology was never created > because pdb2gmx could not write a topology for KAC. > > CHARMM36 does support KAC, but not as a standalone residue. In CHARMM, > one would generate a normal lysine then patch it with the KAC patch. To > make this work in GROMACS, one would have to create a KAC .rtp entry by > applying the same logic - modify LYS according to the KAC patch (found > in the stream/prot/toppar_all36_prot_modify_res.str file from the > tarball distributed by Alex MacKerell: > http://mackerell.umaryland.edu/charmm_ff.shtml#charmm). > > -Justin > > > On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, < > 177cy500.bra...@nitk.edu.in> > > wrote: > > > >> Hi > >> In your tool.top file the particular lys molecule residue name you > >> have to modify. Then it will work..Actually grompp can't find the > molecule > >> in the topology. > >> > >> On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, wrote: > >> > >>> Hi gromacs users, > >>> > >>> I want to simulate a protein where one of the lysine residues is > modified > >>> to acetylated lysine and has been denoted by KAC. I want to simulate > it by > >>> CharmM 36 ff, but it gave me this error. > >>> > >>> > >>> Program gmx pdb2gmx, VERSION 5.1.4 > >>> Source code file: > >>> /home/chip/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c,
Re: [gmx-users] Residue not found in topology
On 8/22/18 5:26 AM, Bratin Kumar Das wrote: Hi In your tool.top file the particular lys molecule residue name you have to modify. Then it will work..Actually grompp can't find the molecule in the topology. The error has nothing to do with grompp. The topology was never created because pdb2gmx could not write a topology for KAC. CHARMM36 does support KAC, but not as a standalone residue. In CHARMM, one would generate a normal lysine then patch it with the KAC patch. To make this work in GROMACS, one would have to create a KAC .rtp entry by applying the same logic - modify LYS according to the KAC patch (found in the stream/prot/toppar_all36_prot_modify_res.str file from the tarball distributed by Alex MacKerell: http://mackerell.umaryland.edu/charmm_ff.shtml#charmm). -Justin On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, <177cy500.bra...@nitk.edu.in> wrote: Hi In your tool.top file the particular lys molecule residue name you have to modify. Then it will work..Actually grompp can't find the molecule in the topology. On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, wrote: Hi gromacs users, I want to simulate a protein where one of the lysine residues is modified to acetylated lysine and has been denoted by KAC. I want to simulate it by CharmM 36 ff, but it gave me this error. Program gmx pdb2gmx, VERSION 5.1.4 Source code file: /home/chip/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c, line: 645 Fatal error: Residue 'KAC' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Is CharmM 36 ff capable to simulate modified residue acetylated lysine? If yes, what is the ff compatible notation for acetylated lysine? If not, which ff can I use to simulate acetylated lysine? Thanks in advance! Amir -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Residue not found in topology
Hi In your tool.top file the particular lys molecule residue name you have to modify. Then it will work..Actually grompp can't find the molecule in the topology. On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, <177cy500.bra...@nitk.edu.in> wrote: > Hi > In your tool.top file the particular lys molecule residue name you > have to modify. Then it will work..Actually grompp can't find the molecule > in the topology. > > On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, wrote: > >> Hi gromacs users, >> >> I want to simulate a protein where one of the lysine residues is modified >> to acetylated lysine and has been denoted by KAC. I want to simulate it by >> CharmM 36 ff, but it gave me this error. >> >> >> Program gmx pdb2gmx, VERSION 5.1.4 >> Source code file: >> /home/chip/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c, >> line: 645 >> >> Fatal error: >> Residue 'KAC' not found in residue topology database >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> >> Is CharmM 36 ff capable to simulate modified residue acetylated lysine? >> If yes, what is the ff compatible notation for acetylated lysine? >> If not, which ff can I use to simulate acetylated lysine? >> >> Thanks in advance! >> >> Amir >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Residue not found in topology
Hi In your tool.top file the particular lys molecule residue name you have to modify. Then it will work..Actually grompp can't find the molecule in the topology. On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, wrote: > Hi gromacs users, > > I want to simulate a protein where one of the lysine residues is modified > to acetylated lysine and has been denoted by KAC. I want to simulate it by > CharmM 36 ff, but it gave me this error. > > > Program gmx pdb2gmx, VERSION 5.1.4 > Source code file: > /home/chip/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c, > line: 645 > > Fatal error: > Residue 'KAC' not found in residue topology database > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > > Is CharmM 36 ff capable to simulate modified residue acetylated lysine? > If yes, what is the ff compatible notation for acetylated lysine? > If not, which ff can I use to simulate acetylated lysine? > > Thanks in advance! > > Amir > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
