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【求助】gromacs的又一个问题
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我运行 gromcs,现在是没有原子数不等的问题了，但是又出现了这个问题： This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description ------------------------------------------------------------ -f minim.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c total.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -deshuf deshuf.ndx Output, Opt. Index file -p sys.top Input Topology file -pp processed.top Output, Opt. Topology file -o input.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -np int 1 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarn int 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes creating statusfile for 1 node... ' for variable optimize_fft, using 'no' Next time use one of: 'no' 'yes' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours for drg 64 turning H bonds into constraints... Excluding 2 bonded neighbours for SOL 218 turning H bonds into constraints... processing coordinates... double-checking input for internal consistency... WARNING 1 [file "sys.top", line 37]: For minimization with LINCS constraints, lincs_iter should be 4 to 8. There was 1 warning ------------------------------------------------------- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 1109 Fatal error: There were 1 error(s) processing your input ------------------------------------------------------- "Jesus Not Only Saves, He Also Frequently Makes Backups." (Myron Bradshaw) 我的sys.top是： ; ; File 'sys.top' was generated ; By user: zhu (503) ; On host: apollo2 ; At date: Wed Mar 12 15:48:05 2008 ; ; This is your topology file ; DRG ; ; Include forcefield parameters #include "ffG53a6.itp" ; Include surfacetant topology #include "drg.itp" ; Include water topology #include "spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name aok in water [ molecules ] ; Compound #mols drg 64 SOL 218 ，而minim.mdp文件为： ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization of AOK ; Title of run ; The following lines tell the program the standard locations where to find cert ain files cpp = /lib/cpp ; Preprocessor include = -I../top ; Directories to include in the topology format ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimizati on) emtol = 1000.0 ; Stop minimization when the maximum force < 3000.0 kJ /mol nsteps = 100000 ; Maximum number of (minimization) steps to perf orm nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout step s xtc_grps = system ; Which coordinate group(s) to write to d isk energygrps = system ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calcul ate the interactions nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, gri d) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interact ions rcoulomb = 1.0 fourierspacing =0.12 pme_order =4 ewald_rtol =1e-5 optimize_fft =yes rvdw = 1.0 ; long range Van der Waals cut-off constraints = hbonds ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) ;freeze ;freezegrps = SOL |
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调剂来这边
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2楼2010-12-22 15:18:04
3楼2010-12-22 16:10:49
4楼2010-12-22 16:54:22
5楼2010-12-22 16:58:39
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static void check_gbsa_params(t_inputrec *ir,gpp_atomtype_t atype) { int nmiss,i; /* If we are doing GBSA, check that we got the parameters we need * This checking is to see if there are GBSA paratmeters for all * atoms in the force field. To go around this for testing purposes * comment out the nerror++ counter temporarily */ nmiss = 0; for(i=0;i if (get_atomtype_radius(i,atype) < 0 || get_atomtype_vol(i,atype) < 0 || get_atomtype_surftens(i,atype) < 0 || get_atomtype_gb_radius(i,atype) < 0 || get_atomtype_S_hct(i,atype) < 0) { fprintf(stderr,"\nGB parameter(s) missing or negative for atom type '%s'\n", get_atomtype_name(i,atype)); nmiss++; } } |
6楼2010-12-22 17:10:30
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zyj8119(金币+1):谢谢参与
zyj8119(金币+1):谢谢参与
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简单回复
matao01114楼
2011-01-01 01:09
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zyj8119(金币+1):谢谢参与
iceem16楼
2011-01-01 23:59
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zyj8119(金币+1):谢谢参与
