Re: [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat
Thnaks for your answer, I have solved the problem with the lacking CD1 atom. There was a weid end of line the line jus before. But pdb2gmx is still unable to link correctly the ZN2 residue with the 4 CYS. The distance between SG and ZN atoms are computed correctly (I have the bon lenght to 0.25 nm) and SG-ZN bonds has been introduced in the topology file. However, pdb2gmx also introduces bonds between the ZN and CB, HB1, HB2 atoms of the 4 Cys, though theses distances don't appear in the distance matrix. I have modified specbond.dat as following : CYS SG 1 ZN2 ZN 1 0.2 CYSZZN2 (previsously : CYS SG 1 ZN2 ZN 4 0.2 CYSZZN2) Supposing that 4 means create 4 bond with, but nothing change. Any suggestion are welcomed! Thanks Nicolas David van der Spoel wrote: Nicolas Sapay wrote: Hello, I'm trying to create a topology file of a system made of a protein homodimer (2x198 residues), water (TIP3P x 900) and some ions (CLA, SOD, ZN2). The system has been initially built with CHARMM and all hydrogens are already included. I use an implementation of CHARMM for Gromacs (i.e. ffcharmm.rtp, .itp, .hdb, .tdb). My objective is to check if it is easy to use pdb files previously built with CHARMM with my implementation of the CHARMM ff in Gromacs. That is why I use a difficult system with dimer, cys-cys bridges, zinc finger, etc... I use the following command to create the topology file: pdb2gmx -f ns5a.pdb -o ns5a.gro -p ns5a.top -water tip3p -ignh -ff charmm27 I have a first problem with the 2 zinc fingers. pdb2gmx find the 2 cys-cys bridges without trouble but failed with the bonds between the ZN2s and the CYSs. I have modified specbond.dat as following: CYS SG 1 ZN2 ZN 4 0.2 CYSZZN2 with ZN2, the residue name of the Zn ion and CYSZ, the residue name for coordinated CYSs. Both residues are defined in ffcharmm27.rtp. However, I haven't found documentation on how to modify specbond.dat. So, I have guessed what the different parameters mean and I'm pretty sure to have done something wrong. Can someone correct my specbond definition and tell me what the different parameters signify? the 0.2 is the bondlength and currently there is a hard toloerance of 10% on that. Check the special bond matrix to see what happens. The second problem comes when pdb2gmx try to add hydrogens. It crashes with the following message : WARNING: atom CD1 not found in residue 84 while adding atom --- Program pdb2gmx, VERSION 3.3.1 Source code file: genhydro.c, line: 304 Fatal error: Atom CD1 not found in residue TRP84 while adding hydrogens --- is your ffcharm27.hdb file correct? since you already have hydrogens you probably don't need to add them. However, the CD1 atom is indeed present in the pdb file and TRP residues upstream to TRP84 are perfectly treated. Additionally HD1 atoms is properly defined in the .hdb file. I have tried to create the .top file on a single monomer and it works perfectly. I have also tried to merge the homodimer using the -merge option of pdb2gmx but it crashes again on the second TRP84... Any suggestion are welcomed! Thanks Nicolas -- [ Nicolas SAPAY, Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University drive NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat
Sorry, the message has been sent too fast, the 4 bonds have been correctly created now. So, the correct specbond line is: CYS SG 1 ZN2 ZN 1 0.25 CYSZZN There is still an angles that lacks (the S-ZN-S angle), but I can add it manually. Nicolas Sorry for the inconvenience Nicolas Nicolas Sapay wrote: Thnaks for your answer, I have solved the problem with the lacking CD1 atom. There was a weid end of line the line jus before. But pdb2gmx is still unable to link correctly the ZN2 residue with the 4 CYS. The distance between SG and ZN atoms are computed correctly (I have the bon lenght to 0.25 nm) and SG-ZN bonds has been introduced in the topology file. However, pdb2gmx also introduces bonds between the ZN and CB, HB1, HB2 atoms of the 4 Cys, though theses distances don't appear in the distance matrix. I have modified specbond.dat as following : CYS SG 1 ZN2 ZN 1 0.2 CYSZZN2 (previsously : CYS SG 1 ZN2 ZN 4 0.2 CYSZZN2) Supposing that 4 means create 4 bond with, but nothing change. Any suggestion are welcomed! Thanks Nicolas David van der Spoel wrote: Nicolas Sapay wrote: Hello, I'm trying to create a topology file of a system made of a protein homodimer (2x198 residues), water (TIP3P x 900) and some ions (CLA, SOD, ZN2). The system has been initially built with CHARMM and all hydrogens are already included. I use an implementation of CHARMM for Gromacs (i.e. ffcharmm.rtp, .itp, .hdb, .tdb). My objective is to check if it is easy to use pdb files previously built with CHARMM with my implementation of the CHARMM ff in Gromacs. That is why I use a difficult system with dimer, cys-cys bridges, zinc finger, etc... I use the following command to create the topology file: pdb2gmx -f ns5a.pdb -o ns5a.gro -p ns5a.top -water tip3p -ignh -ff charmm27 I have a first problem with the 2 zinc fingers. pdb2gmx find the 2 cys-cys bridges without trouble but failed with the bonds between the ZN2s and the CYSs. I have modified specbond.dat as following: CYS SG 1 ZN2 ZN 4 0.2 CYSZZN2 with ZN2, the residue name of the Zn ion and CYSZ, the residue name for coordinated CYSs. Both residues are defined in ffcharmm27.rtp. However, I haven't found documentation on how to modify specbond.dat. So, I have guessed what the different parameters mean and I'm pretty sure to have done something wrong. Can someone correct my specbond definition and tell me what the different parameters signify? the 0.2 is the bondlength and currently there is a hard toloerance of 10% on that. Check the special bond matrix to see what happens. The second problem comes when pdb2gmx try to add hydrogens. It crashes with the following message : WARNING: atom CD1 not found in residue 84 while adding atom --- Program pdb2gmx, VERSION 3.3.1 Source code file: genhydro.c, line: 304 Fatal error: Atom CD1 not found in residue TRP84 while adding hydrogens --- is your ffcharm27.hdb file correct? since you already have hydrogens you probably don't need to add them. However, the CD1 atom is indeed present in the pdb file and TRP residues upstream to TRP84 are perfectly treated. Additionally HD1 atoms is properly defined in the .hdb file. I have tried to create the .top file on a single monomer and it works perfectly. I have also tried to merge the homodimer using the -merge option of pdb2gmx but it crashes again on the second TRP84... Any suggestion are welcomed! Thanks Nicolas -- [ Nicolas SAPAY, Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University drive NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat
Hi Nicolas, Have a look at the ff*bon.itp of your choice and go all the way to the bottom. You can see there how the connections are handled further for e.g. heme and can add the angles and dihedrals you want. Also, you report bonds between the zinc and a number of other atoms. This is probably due to the viewer you use, which bases connectivity on the distances between atoms. This has nothing to do with a topology. Cheers, Tsjerk On 5/15/07, Nicolas Sapay [EMAIL PROTECTED] wrote: Sorry, the message has been sent too fast, the 4 bonds have been correctly created now. So, the correct specbond line is: CYS SG 1 ZN2 ZN 1 0.25 CYSZZN There is still an angles that lacks (the S-ZN-S angle), but I can add it manually. Nicolas Sorry for the inconvenience Nicolas Nicolas Sapay wrote: Thnaks for your answer, I have solved the problem with the lacking CD1 atom. There was a weid end of line the line jus before. But pdb2gmx is still unable to link correctly the ZN2 residue with the 4 CYS. The distance between SG and ZN atoms are computed correctly (I have the bon lenght to 0.25 nm) and SG-ZN bonds has been introduced in the topology file. However, pdb2gmx also introduces bonds between the ZN and CB, HB1, HB2 atoms of the 4 Cys, though theses distances don't appear in the distance matrix. I have modified specbond.dat as following : CYS SG 1 ZN2 ZN 1 0.2 CYSZZN2 (previsously : CYS SG 1 ZN2 ZN 4 0.2 CYSZZN2) Supposing that 4 means create 4 bond with, but nothing change. Any suggestion are welcomed! Thanks Nicolas David van der Spoel wrote: Nicolas Sapay wrote: Hello, I'm trying to create a topology file of a system made of a protein homodimer (2x198 residues), water (TIP3P x 900) and some ions (CLA, SOD, ZN2). The system has been initially built with CHARMM and all hydrogens are already included. I use an implementation of CHARMM for Gromacs (i.e. ffcharmm.rtp, .itp, .hdb, .tdb). My objective is to check if it is easy to use pdb files previously built with CHARMM with my implementation of the CHARMM ff in Gromacs. That is why I use a difficult system with dimer, cys-cys bridges, zinc finger, etc... I use the following command to create the topology file: pdb2gmx -f ns5a.pdb -o ns5a.gro -p ns5a.top -water tip3p -ignh -ff charmm27 I have a first problem with the 2 zinc fingers. pdb2gmx find the 2 cys-cys bridges without trouble but failed with the bonds between the ZN2s and the CYSs. I have modified specbond.dat as following: CYS SG 1 ZN2 ZN 4 0.2 CYSZZN2 with ZN2, the residue name of the Zn ion and CYSZ, the residue name for coordinated CYSs. Both residues are defined in ffcharmm27.rtp. However, I haven't found documentation on how to modify specbond.dat. So, I have guessed what the different parameters mean and I'm pretty sure to have done something wrong. Can someone correct my specbond definition and tell me what the different parameters signify? the 0.2 is the bondlength and currently there is a hard toloerance of 10% on that. Check the special bond matrix to see what happens. The second problem comes when pdb2gmx try to add hydrogens. It crashes with the following message : WARNING: atom CD1 not found in residue 84 while adding atom --- Program pdb2gmx, VERSION 3.3.1 Source code file: genhydro.c, line: 304 Fatal error: Atom CD1 not found in residue TRP84 while adding hydrogens --- is your ffcharm27.hdb file correct? since you already have hydrogens you probably don't need to add them. However, the CD1 atom is indeed present in the pdb file and TRP residues upstream to TRP84 are perfectly treated. Additionally HD1 atoms is properly defined in the .hdb file. I have tried to create the .top file on a single monomer and it works perfectly. I have also tried to merge the homodimer using the -merge option of pdb2gmx but it crashes again on the second TRP84... Any suggestion are welcomed! Thanks Nicolas -- [ Nicolas SAPAY, Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University drive NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
Re: [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat
Nicolas Sapay wrote: Hello, I'm trying to create a topology file of a system made of a protein homodimer (2x198 residues), water (TIP3P x 900) and some ions (CLA, SOD, ZN2). The system has been initially built with CHARMM and all hydrogens are already included. I use an implementation of CHARMM for Gromacs (i.e. ffcharmm.rtp, .itp, .hdb, .tdb). My objective is to check if it is easy to use pdb files previously built with CHARMM with my implementation of the CHARMM ff in Gromacs. That is why I use a difficult system with dimer, cys-cys bridges, zinc finger, etc... I use the following command to create the topology file: pdb2gmx -f ns5a.pdb -o ns5a.gro -p ns5a.top -water tip3p -ignh -ff charmm27 I have a first problem with the 2 zinc fingers. pdb2gmx find the 2 cys-cys bridges without trouble but failed with the bonds between the ZN2s and the CYSs. I have modified specbond.dat as following: CYS SG 1 ZN2 ZN 4 0.2 CYSZZN2 with ZN2, the residue name of the Zn ion and CYSZ, the residue name for coordinated CYSs. Both residues are defined in ffcharmm27.rtp. However, I haven't found documentation on how to modify specbond.dat. So, I have guessed what the different parameters mean and I'm pretty sure to have done something wrong. Can someone correct my specbond definition and tell me what the different parameters signify? the 0.2 is the bondlength and currently there is a hard toloerance of 10% on that. Check the special bond matrix to see what happens. The second problem comes when pdb2gmx try to add hydrogens. It crashes with the following message : WARNING: atom CD1 not found in residue 84 while adding atom --- Program pdb2gmx, VERSION 3.3.1 Source code file: genhydro.c, line: 304 Fatal error: Atom CD1 not found in residue TRP84 while adding hydrogens --- is your ffcharm27.hdb file correct? since you already have hydrogens you probably don't need to add them. However, the CD1 atom is indeed present in the pdb file and TRP residues upstream to TRP84 are perfectly treated. Additionally HD1 atoms is properly defined in the .hdb file. I have tried to create the .top file on a single monomer and it works perfectly. I have also tried to merge the homodimer using the -merge option of pdb2gmx but it crashes again on the second TRP84... Any suggestion are welcomed! Thanks Nicolas -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat
Hello, I'm trying to create a topology file of a system made of a protein homodimer (2x198 residues), water (TIP3P x 900) and some ions (CLA, SOD, ZN2). The system has been initially built with CHARMM and all hydrogens are already included. I use an implementation of CHARMM for Gromacs (i.e. ffcharmm.rtp, .itp, .hdb, .tdb). My objective is to check if it is easy to use pdb files previously built with CHARMM with my implementation of the CHARMM ff in Gromacs. That is why I use a difficult system with dimer, cys-cys bridges, zinc finger, etc... I use the following command to create the topology file: pdb2gmx -f ns5a.pdb -o ns5a.gro -p ns5a.top -water tip3p -ignh -ff charmm27 I have a first problem with the 2 zinc fingers. pdb2gmx find the 2 cys-cys bridges without trouble but failed with the bonds between the ZN2s and the CYSs. I have modified specbond.dat as following: CYS SG 1 ZN2 ZN 4 0.2 CYSZZN2 with ZN2, the residue name of the Zn ion and CYSZ, the residue name for coordinated CYSs. Both residues are defined in ffcharmm27.rtp. However, I haven't found documentation on how to modify specbond.dat. So, I have guessed what the different parameters mean and I'm pretty sure to have done something wrong. Can someone correct my specbond definition and tell me what the different parameters signify? The second problem comes when pdb2gmx try to add hydrogens. It crashes with the following message : WARNING: atom CD1 not found in residue 84 while adding atom --- Program pdb2gmx, VERSION 3.3.1 Source code file: genhydro.c, line: 304 Fatal error: Atom CD1 not found in residue TRP84 while adding hydrogens --- However, the CD1 atom is indeed present in the pdb file and TRP residues upstream to TRP84 are perfectly treated. Additionally HD1 atoms is properly defined in the .hdb file. I have tried to create the .top file on a single monomer and it works perfectly. I have also tried to merge the homodimer using the -merge option of pdb2gmx but it crashes again on the second TRP84... Any suggestion are welcomed! Thanks Nicolas -- [ Nicolas SAPAY, Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University drive NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
