Custom Search
-- Amy He Chemistry Graduate Teaching Assistant Hadad Lab Ohio State University he.1768.osu.edu<mailto:he.1768.osu.edu> From: MD MUZAFFAR UR REHMAN via AMBER <amber.ambermd.org> Date: Monday, October 23, 2023 at 1:26 AM To: David A Case <dacase1.gmail.com> Cc: AMBER Mailing List <amber.ambermd.org> Subject: Re: [AMBER] Error with tleap: Atom does not have a type Thanks for your response. I am actually carrying out the entropy calculations by generating the ligand and protein topologies via intermol (converting out.cms to gromacs file and its topology files). Using the generated topology files for both ligand and protein, I run the gmxMMPBSA command and I end up with tleap error. I have followed tutorial 2.1 from amber tutorials, but even after generating a new unit "LIG" (also its lib file was generated), the problem persists. I have not attached in the initial steps because of the lengthy mail. (Green color bold texts are the commands I have given by following the tutorial) *$ tleap -f oldff/leaprc.ff99SB* -I: Adding /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/prep to search path. -I: Adding /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/lib to search path. -I: Adding /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/parm to search path. -I: Adding /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/cmd to search path. -f: Source oldff/leaprc.ff99SB. Welcome to LEaP! (no leaprc in search path) Sourcing: /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/cmd/oldff/leaprc.ff99SB Log file: ./leap.log Loading parameters: /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, Polariz.& LP incl.02/04/99 Loading parameters: /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) Loading library: /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/lib/all_nucleic94.lib Loading library: /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/lib/all_amino94.lib Loading library: /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/lib/all_aminoct94.lib Loading library: /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/lib/all_aminont94.lib Loading library: /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/lib/ions94.lib Loading library: /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/lib/solvents.lib *> source leaprc.gaff* ----- Source: /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/cmd/leaprc.gaff ----- Source of /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/cmd/leaprc.gaff done Log file: ./leap.log Loading parameters: /home/mb_uzair/miniconda3/envs/gmxMMPBSA/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) *> LIG - loadmol2 ligand.mol2* Warning: Couldn't scan NUMBER from (-) Error: Error from the parser: syntax error *> LIG = loadmol2 ligand.mol2* Loading Mol2 file: ./ligand.mol2 Reading MOLECULE named LIG *> list* ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CCYX CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CILE CIO CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX Cl- Cs+ DA DA3 DA5 DAN DC DC3 DC4 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN FB3 FB3BOX FB4 FB4BOX GLH GLN GLU GLY HID HIE HIP HIS HOH IB ILE K+ LEU LIG LYN LYS Li+ MEOHBOX MET MG2 NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ OP3 OPC OPC3BOX OPCBOX PHE PL3 POL3BOX PRO QSPCFWBOX RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOX TIP5PBOX TP3 TP4 TP5 TPF TRP TYR VAL WAT frcmod99SBgaff parm99 *> check LIG* Checking 'LIG'.... Checking parameters for unit 'LIG'. Checking for bond parameters. Checking for angle parameters. Unit is OK. *> loadamberparams ligand.frcmod* Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here *> check LIG* Checking 'LIG'.... Checking parameters for unit 'LIG'. Checking for bond parameters. Checking for angle parameters. Unit is OK. *> saveoff LIG lig.lib* Creating lig.lib Building topology. Building atom parameters. *> saveamberparam LIG ligand.prmtop ligand.rst7* Error: Error from the parser: syntax error --------------------------------------------------after this, I have run the gmxMMPBSA command, and the leap.log files shows the following error again:---------------------------------------- > LIG1 = loadpdb _GMXMMPBSA_LIG_F1.pdb Loading PDB file: ./_GMXMMPBSA_LIG_F1.pdb Matching PDB residue names to LEaP variables. /home/mb_uzair/miniconda3/envs/gmxMMPBSA/bin/teLeap: Warning! Unknown residue: LIG number: 0 type: Terminal/last ..relaxing end constraints to try for a dbase match /home/mb_uzair/miniconda3/envs/gmxMMPBSA/bin/teLeap: Warning! -no luck Creating new UNIT for residue: LIG sequence: 900 Created a new atom named: O1 within residue: .R<LIG 900> Created a new atom named: P1 within residue: .R<LIG 900> Created a new atom named: C1 within residue: .R<LIG 900> Created a new atom named: N1 within residue: .R<LIG 900> Created a new atom named: C2 within residue: .R<LIG 900> Created a new atom named: C3 within residue: .R<LIG 900> Created a new atom named: C4 within residue: .R<LIG 900> Created a new atom named: C5 within residue: .R<LIG 900> Created a new atom named: C6 within residue: .R<LIG 900> Created a new atom named: C7 within residue: .R<LIG 900> Created a new atom named: C8 within residue: .R<LIG 900> Created a new atom named: C9 within residue: .R<LIG 900> Created a new atom named: C10 within residue: .R<LIG 900> Created a new atom named: N2 within residue: .R<LIG 900> Created a new atom named: P2 within residue: .R<LIG 900> Created a new atom named: O2 within residue: .R<LIG 900> Created a new atom named: O3 within residue: .R<LIG 900> Created a new atom named: O4 within residue: .R<LIG 900> Created a new atom named: O5 within residue: .R<LIG 900> Created a new atom named: O6 within residue: .R<LIG 900> total atoms in file: 20 The file contained 20 atoms not in residue templates > LIG_OUT = combine { LIG1 } Sequence: default_name > saveamberparm LIG_OUT LIG.prmtop _GMXMMPBSA_LIG.inpcrd Checking Unit. FATAL: Atom .R<LIG 900>.A<O6 20> does not have a type. FATAL: Atom .R<LIG 900>.A<O5 19> does not have a type. FATAL: Atom .R<LIG 900>.A<O4 18> does not have a type. FATAL: Atom .R<LIG 900>.A<O3 17> does not have a type. FATAL: Atom .R<LIG 900>.A<O2 16> does not have a type. FATAL: Atom .R<LIG 900>.A<P2 15> does not have a type. FATAL: Atom .R<LIG 900>.A<N2 14> does not have a type. FATAL: Atom .R<LIG 900>.A<C10 13> does not have a type. FATAL: Atom .R<LIG 900>.A<C9 12> does not have a type. FATAL: Atom .R<LIG 900>.A<C8 11> does not have a type. FATAL: Atom .R<LIG 900>.A<C7 10> does not have a type. FATAL: Atom .R<LIG 900>.A<C6 9> does not have a type. FATAL: Atom .R<LIG 900>.A<C5 8> does not have a type. FATAL: Atom .R<LIG 900>.A<C4 7> does not have a type. FATAL: Atom .R<LIG 900>.A<C3 6> does not have a type. FATAL: Atom .R<LIG 900>.A<C2 5> does not have a type. FATAL: Atom .R<LIG 900>.A<N1 4> does not have a type. FATAL: Atom .R<LIG 900>.A<C1 3> does not have a type. FATAL: Atom .R<LIG 900>.A<P1 2> does not have a type. FATAL: Atom .R<LIG 900>.A<O1 1> does not have a type. /home/mb_uzair/miniconda3/envs/gmxMMPBSA/bin/teLeap: Fatal Error! Failed to generate parameters Exiting LEaP: Errors = 1; Warnings = 2; Notes = 0. Please guide me through this. Thanks & Regards, MD Muzaffar Ur Rehman, *Research Scholar* Department of Pharmacy BITS-Pilani, Pilani campus, Rajasthan. Alternate_email: muzaffar.rehman.pilani.bits-pilani.ac.in m.muzaffar687.gmail.com Contact: +91-8686294437. [image: Mailtrack] <https://urldefense.com/v3/__https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&__;!!KGKeukY!yi1Sr8J2hD8rQ-V5akegFuPSEjRNnG2tGpr6iGp3Q2OdNRs89l6zqmYJyuGACi6XW1ysyNnWF2j7VxDJcV-WnHdGAys$ > Sender notified by Mailtrack <https://urldefense.com/v3/__https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&__;!!KGKeukY!yi1Sr8J2hD8rQ-V5akegFuPSEjRNnG2tGpr6iGp3Q2OdNRs89l6zqmYJyuGACi6XW1ysyNnWF2j7VxDJcV-WnHdGAys$ > 10/23/23, 10:46:20 AM On Thu, Oct 19, 2023 at 9:08 PM David A Case <dacase1.gmail.com> wrote: > On Fri, Oct 13, 2023, MD MUZAFFAR UR REHMAN via AMBER wrote: > > >"> LIG1 = loadpdb _GMXMMPBSA_LIG_F1.pdb > >Creating new UNIT for residue: LIG sequence: 900 > >Created a new atom named: O1 within residue: .R<LIG 900> > > It looks like you have not created a unit named "LIG" that matches what is > in your PDB file. Note that "LIG" is a general name for an unspecified > ligand -- you need to create and load a unit in order for tleap to know how > to handle it. > > See Tutorial 2.1 at the Amber web site for basic instructions here. > > ...dac > > -- The information contained in this electronic communication is intended solely for the individual(s) or entity to which it is addressed. It may contain proprietary, confidential and/or legally privileged information. Any review, retransmission, dissemination, printing, copying or other use of, or taking any action in reliance on the contents of this information by person(s) or entities other than the intended recipient is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us by responding to this email or telephone and immediately and permanently delete all copies of this message and any attachments from your system(s). The contents of this message do not necessarily represent the views or policies of BITS Pilani. _______________________________________________ AMBER mailing list AMBER.ambermd.org https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!yi1Sr8J2hD8rQ-V5akegFuPSEjRNnG2tGpr6iGp3Q2OdNRs89l6zqmYJyuGACi6XW1ysyNnWF2j7VxDJcV-W0WEnl-E$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!yi1Sr8J2hD8rQ-V5akegFuPSEjRNnG2tGpr6iGp3Q2OdNRs89l6zqmYJyuGACi6XW1ysyNnWF2j7VxDJcV-W0WEnl-E$> _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Oct 22 2023 - 23:00:07 PDT