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From: Carlos Simmerling via AMBER <amber.ambermd.org>

Date: Fri, 20 Jan 2023 17:54:47 -0500

did your original pdb file have hydrogen atoms? the names in the error

messages appear to be non-standard. if they were in the original file, I'm

not sure how it could have worked in gas phase either. you can try removing

H atoms, using pdb4amber or cpptraj's prepareforleap, but make sure you

look into the details to know if this indeed is the (only) problem.

On Fri, Jan 20, 2023 at 5:47 PM laura zhang via AMBER <amber.ambermd.org>

wrote:

*> Dear Amber users,
*

*>
*

*> I tried to set up a protein bound with a ligand simulation. In the tleap
*

*> step, I got the following error message:
*

*>
*

*> /amber20/bin/teLeap: Warning!
*

*> The unperturbed charge of the unit (-5.000000) is not zero.
*

*> FATAL: Atom .R<CARG 530>.A<HD1 29> does not have a type.
*

*> FATAL: Atom .R<CARG 530>.A<HG1 28> does not have a type.
*

*> FATAL: Atom .R<CARG 530>.A<HB1 27> does not have a type.
*

*> FATAL: Atom .R<CARG 530>.A<HN 26> does not have a type.
*

*> FATAL: Atom .R<SER 529>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 529>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 529>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<ARG 528>.A<HD1 28> does not have a type.
*

*> FATAL: Atom .R<ARG 528>.A<HG1 27> does not have a type.
*

*> FATAL: Atom .R<ARG 528>.A<HB1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 528>.A<HN 25> does not have a type.
*

*> FATAL: Atom .R<CYX 527>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 527>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<CYX 526>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 526>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<ILE 525>.A<HD3 25> does not have a type.
*

*> FATAL: Atom .R<ILE 525>.A<HD2 24> does not have a type.
*

*> FATAL: Atom .R<ILE 525>.A<HD1 23> does not have a type.
*

*> FATAL: Atom .R<ILE 525>.A<CD 22> does not have a type.
*

*> FATAL: Atom .R<ILE 525>.A<HG11 21> does not have a type.
*

*> FATAL: Atom .R<ILE 525>.A<HN 20> does not have a type.
*

*> FATAL: Atom .R<ALA 524>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<VAL 523>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<ALA 522>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<THR 521>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<VAL 520>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<ALA 519>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<GLY 518>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 518>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<GLU 517>.A<HG1 18> does not have a type.
*

*> FATAL: Atom .R<GLU 517>.A<HB1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 517>.A<HN 16> does not have a type.
*

*> FATAL: Atom .R<SER 516>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 516>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 516>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<THR 515>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<SER 514>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 514>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 514>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<GLY 513>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 513>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<THR 512>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<THR 511>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<SER 510>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 510>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 510>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<VAL 509>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<ASP 508>.A<HB1 14> does not have a type.
*

*> FATAL: Atom .R<ASP 508>.A<HN 13> does not have a type.
*

*> FATAL: Atom .R<ARG 507>.A<HD1 28> does not have a type.
*

*> FATAL: Atom .R<ARG 507>.A<HG1 27> does not have a type.
*

*> FATAL: Atom .R<ARG 507>.A<HB1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 507>.A<HN 25> does not have a type.
*

*> FATAL: Atom .R<SER 506>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 506>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 506>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<ARG 505>.A<HD1 28> does not have a type.
*

*> FATAL: Atom .R<ARG 505>.A<HG1 27> does not have a type.
*

*> FATAL: Atom .R<ARG 505>.A<HB1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 505>.A<HN 25> does not have a type.
*

*> FATAL: Atom .R<VAL 504>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<VAL 503>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<CYX 502>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 502>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<THR 501>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<ASN 500>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<ASN 500>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<ASP 499>.A<HB1 14> does not have a type.
*

*> FATAL: Atom .R<ASP 499>.A<HN 13> does not have a type.
*

*> FATAL: Atom .R<VAL 498>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<ALA 497>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<TYR 496>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<TYR 496>.A<HN 22> does not have a type.
*

*> FATAL: Atom .R<ALA 495>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<GLY 494>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 494>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<LEU 493>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<LEU 493>.A<HN 20> does not have a type.
*

*> FATAL: Atom .R<VAL 492>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<HID 491>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<HID 491>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<SER 490>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 490>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 490>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<THR 489>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<GLY 488>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 488>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<PRO 487>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 487>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 487>.A<HD1 15> does not have a type.
*

*> FATAL: Atom .R<LEU 486>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<LEU 486>.A<HN 20> does not have a type.
*

*> FATAL: Atom .R<ALA 485>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<SER 484>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 484>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 484>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<CYX 483>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 483>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<GLY 482>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 482>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<THR 481>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<LEU 480>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<LEU 480>.A<HN 20> does not have a type.
*

*> FATAL: Atom .R<THR 479>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<TRP 478>.A<HB1 26> does not have a type.
*

*> FATAL: Atom .R<TRP 478>.A<HN 25> does not have a type.
*

*> FATAL: Atom .R<GLY 477>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 477>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<GLU 476>.A<HG1 18> does not have a type.
*

*> FATAL: Atom .R<GLU 476>.A<HB1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 476>.A<HN 16> does not have a type.
*

*> FATAL: Atom .R<GLU 475>.A<HG1 18> does not have a type.
*

*> FATAL: Atom .R<GLU 475>.A<HB1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 475>.A<HN 16> does not have a type.
*

*> FATAL: Atom .R<CYX 474>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 474>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<ALA 473>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<VAL 472>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<THR 471>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<VAL 470>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<GLN 469>.A<HG1 20> does not have a type.
*

*> FATAL: Atom .R<GLN 469>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<GLN 469>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<GLU 468>.A<HG1 18> does not have a type.
*

*> FATAL: Atom .R<GLU 468>.A<HB1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 468>.A<HN 16> does not have a type.
*

*> FATAL: Atom .R<GLN 467>.A<HG1 20> does not have a type.
*

*> FATAL: Atom .R<GLN 467>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<GLN 467>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<PRO 466>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 466>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 466>.A<HD1 15> does not have a type.
*

*> FATAL: Atom .R<ALA 465>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<PRO 464>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 464>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 464>.A<HD1 15> does not have a type.
*

*> FATAL: Atom .R<ILE 463>.A<HD3 25> does not have a type.
*

*> FATAL: Atom .R<ILE 463>.A<HD2 24> does not have a type.
*

*> FATAL: Atom .R<ILE 463>.A<HD1 23> does not have a type.
*

*> FATAL: Atom .R<ILE 463>.A<CD 22> does not have a type.
*

*> FATAL: Atom .R<ILE 463>.A<HG11 21> does not have a type.
*

*> FATAL: Atom .R<ILE 463>.A<HN 20> does not have a type.
*

*> FATAL: Atom .R<GLY 462>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 462>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<HID 461>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<HID 461>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<GLU 460>.A<HG1 18> does not have a type.
*

*> FATAL: Atom .R<GLU 460>.A<HB1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 460>.A<HN 16> does not have a type.
*

*> FATAL: Atom .R<LYS 459>.A<HE1 27> does not have a type.
*

*> FATAL: Atom .R<LYS 459>.A<HD1 26> does not have a type.
*

*> FATAL: Atom .R<LYS 459>.A<HG1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 459>.A<HB1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 459>.A<HN 23> does not have a type.
*

*> FATAL: Atom .R<VAL 458>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<LYS 457>.A<HE1 27> does not have a type.
*

*> FATAL: Atom .R<LYS 457>.A<HD1 26> does not have a type.
*

*> FATAL: Atom .R<LYS 457>.A<HG1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 457>.A<HB1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 457>.A<HN 23> does not have a type.
*

*> FATAL: Atom .R<CYX 456>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 456>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<GLU 455>.A<HG1 18> does not have a type.
*

*> FATAL: Atom .R<GLU 455>.A<HB1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 455>.A<HN 16> does not have a type.
*

*> FATAL: Atom .R<LEU 454>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<LEU 454>.A<HN 20> does not have a type.
*

*> FATAL: Atom .R<GLY 453>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 453>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<PRO 452>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 452>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 452>.A<HD1 15> does not have a type.
*

*> FATAL: Atom .R<ALA 451>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<HID 450>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<HID 450>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<CYX 449>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 449>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<CYX 448>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 448>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<SER 447>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 447>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 447>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<ALA 446>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<HID 445>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<HID 445>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<ILE 444>.A<HD3 25> does not have a type.
*

*> FATAL: Atom .R<ILE 444>.A<HD2 24> does not have a type.
*

*> FATAL: Atom .R<ILE 444>.A<HD1 23> does not have a type.
*

*> FATAL: Atom .R<ILE 444>.A<CD 22> does not have a type.
*

*> FATAL: Atom .R<ILE 444>.A<HG11 21> does not have a type.
*

*> FATAL: Atom .R<ILE 444>.A<HN 20> does not have a type.
*

*> FATAL: Atom .R<SER 443>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 443>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 443>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<ALA 442>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<GLU 441>.A<HG1 18> does not have a type.
*

*> FATAL: Atom .R<GLU 441>.A<HB1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 441>.A<HN 16> does not have a type.
*

*> FATAL: Atom .R<ARG 440>.A<HD1 28> does not have a type.
*

*> FATAL: Atom .R<ARG 440>.A<HG1 27> does not have a type.
*

*> FATAL: Atom .R<ARG 440>.A<HB1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 440>.A<HN 25> does not have a type.
*

*> FATAL: Atom .R<HID 439>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<HID 439>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<GLY 438>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 438>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<VAL 437>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<CYX 436>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 436>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<GLN 435>.A<HG1 20> does not have a type.
*

*> FATAL: Atom .R<GLN 435>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<GLN 435>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<ASN 434>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<ASN 434>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<PRO 433>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 433>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 433>.A<HD1 15> does not have a type.
*

*> FATAL: Atom .R<GLN 432>.A<HG1 20> does not have a type.
*

*> FATAL: Atom .R<GLN 432>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<GLN 432>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<GLY 431>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 431>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<ARG 430>.A<HD1 28> does not have a type.
*

*> FATAL: Atom .R<ARG 430>.A<HG1 27> does not have a type.
*

*> FATAL: Atom .R<ARG 430>.A<HB1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 430>.A<HN 25> does not have a type.
*

*> FATAL: Atom .R<PRO 429>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 429>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 429>.A<HD1 15> does not have a type.
*

*> FATAL: Atom .R<ARG 428>.A<HD1 28> does not have a type.
*

*> FATAL: Atom .R<ARG 428>.A<HG1 27> does not have a type.
*

*> FATAL: Atom .R<ARG 428>.A<HB1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 428>.A<HN 25> does not have a type.
*

*> FATAL: Atom .R<LEU 427>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<LEU 427>.A<HN 20> does not have a type.
*

*> FATAL: Atom .R<VAL 426>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<PRO 425>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 425>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 425>.A<HD1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 424>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 424>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 424>.A<HD1 15> does not have a type.
*

*> FATAL: Atom .R<LYS 423>.A<HE1 27> does not have a type.
*

*> FATAL: Atom .R<LYS 423>.A<HD1 26> does not have a type.
*

*> FATAL: Atom .R<LYS 423>.A<HG1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 423>.A<HB1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 423>.A<HN 23> does not have a type.
*

*> FATAL: Atom .R<HID 422>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<HID 422>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<THR 421>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<GLY 420>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 420>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<LEU 419>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<LEU 419>.A<HN 20> does not have a type.
*

*> FATAL: Atom .R<ASP 418>.A<HB1 14> does not have a type.
*

*> FATAL: Atom .R<ASP 418>.A<HN 13> does not have a type.
*

*> FATAL: Atom .R<GLU 417>.A<HG1 18> does not have a type.
*

*> FATAL: Atom .R<GLU 417>.A<HB1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 417>.A<HN 16> does not have a type.
*

*> FATAL: Atom .R<VAL 416>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<GLU 415>.A<HG1 18> does not have a type.
*

*> FATAL: Atom .R<GLU 415>.A<HB1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 415>.A<HN 16> does not have a type.
*

*> FATAL: Atom .R<TRP 414>.A<HB1 26> does not have a type.
*

*> FATAL: Atom .R<TRP 414>.A<HN 25> does not have a type.
*

*> FATAL: Atom .R<HID 413>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<HID 413>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<SER 412>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 412>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 412>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<SER 411>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 411>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 411>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<CYX 410>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 410>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<GLY 409>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 409>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<THR 408>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<LEU 407>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<LEU 407>.A<HN 20> does not have a type.
*

*> FATAL: Atom .R<VAL 406>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<HID 405>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<HID 405>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<GLY 404>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 404>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<GLN 403>.A<HG1 20> does not have a type.
*

*> FATAL: Atom .R<GLN 403>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<GLN 403>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<GLN 402>.A<HG1 20> does not have a type.
*

*> FATAL: Atom .R<GLN 402>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<GLN 402>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<HID 401>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<HID 401>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<CYX 400>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 400>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<HID 399>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<HID 399>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<VAL 398>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<ARG 397>.A<HD1 28> does not have a type.
*

*> FATAL: Atom .R<ARG 397>.A<HG1 27> does not have a type.
*

*> FATAL: Atom .R<ARG 397>.A<HB1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 397>.A<HN 25> does not have a type.
*

*> FATAL: Atom .R<THR 396>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<GLY 395>.A<HA1 9> does not have a type.
*

*> FATAL: Atom .R<GLY 395>.A<HN 8> does not have a type.
*

*> FATAL: Atom .R<MET 394>.A<HG1 20> does not have a type.
*

*> FATAL: Atom .R<MET 394>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<MET 394>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<SER 393>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 393>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 393>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<ALA 392>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<GLU 391>.A<HG1 18> does not have a type.
*

*> FATAL: Atom .R<GLU 391>.A<HB1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 391>.A<HN 16> does not have a type.
*

*> FATAL: Atom .R<ALA 390>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<PRO 389>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 389>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 389>.A<HD1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 388>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 388>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 388>.A<HD1 15> does not have a type.
*

*> FATAL: Atom .R<ALA 387>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<THR 386>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<HID 385>.A<HB1 19> does not have a type.
*

*> FATAL: Atom .R<HID 385>.A<HN 18> does not have a type.
*

*> FATAL: Atom .R<VAL 384>.A<HN 17> does not have a type.
*

*> FATAL: Atom .R<SER 383>.A<HG1 14> does not have a type.
*

*> FATAL: Atom .R<SER 383>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 383>.A<HN 12> does not have a type.
*

*> FATAL: Atom .R<CYX 382>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<CYX 382>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<ASN 381>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<ASN 381>.A<HN 15> does not have a type.
*

*> FATAL: Atom .R<ALA 380>.A<HN 11> does not have a type.
*

*> FATAL: Atom .R<GLN 379>.A<HG1 20> does not have a type
*

*>
*

*>
*

*> I am wondering where is wrong. In fact, the protein complex in gas phase
*

*> pdb file was generated without any problem in the tleap step, although the
*

*> parm7 file could not be generated. The following was copied from the
*

*> related tleap script:
*

*>
*

*> gascomplex= combine {rec lig}
*

*>
*

*> savepdb gascomplex pcsk.gas.complex.pdb
*

*> saveamberparm gascomplex pcsk.complex.parm7 pcsk.gas.complex.rst7
*

*>
*

*> I am wondering where is wrong. One observation is that the original
*

*> protein pdb file has the residue number starting from 2, while the
*

*> pcsk.gas.complex.pdb file has the protein residue number starting from 1.
*

*> Will that contribute to the error? I can attach the whole output from
*

*> tleap run and the pcsk.gas.complex.pdb file if they are useful. Thank you
*

*> very much.
*

*>
*

*>
*

*> Laura
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Fri Jan 20 2023 - 15:00:06 PST

Date: Fri, 20 Jan 2023 17:54:47 -0500

did your original pdb file have hydrogen atoms? the names in the error

messages appear to be non-standard. if they were in the original file, I'm

not sure how it could have worked in gas phase either. you can try removing

H atoms, using pdb4amber or cpptraj's prepareforleap, but make sure you

look into the details to know if this indeed is the (only) problem.

On Fri, Jan 20, 2023 at 5:47 PM laura zhang via AMBER <amber.ambermd.org>

wrote:

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Received on Fri Jan 20 2023 - 15:00:06 PST

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